diff --git a/common/arg.cpp b/common/arg.cpp
index 152f671ab..4b34aee0e 100644
--- a/common/arg.cpp
+++ b/common/arg.cpp
@@ -1975,6 +1975,17 @@ common_params_context common_params_parser_init(common_params & params, llama_ex
             params.use_jinja = true;
         }
     ).set_examples({LLAMA_EXAMPLE_SERVER, LLAMA_EXAMPLE_MAIN}).set_env("LLAMA_ARG_JINJA"));
+    add_opt(common_arg(
+        {"--reasoning-format"}, "FORMAT",
+        "reasoning format (default: deepseek; allowed values: deepseek, none)\n"
+        "controls whether thought tags are extracted from the response, and in which format they're returned. 'none' leaves thoughts unparsed in `message.content`, 'deepseek' puts them in `message.reasoning_content` (for DeepSeek R1 & Command R7B only).\n"
+        "only supported for non-streamed responses",
+        [](common_params & params, const std::string & value) {
+            /**/ if (value == "deepseek") { params.reasoning_format = COMMON_REASONING_FORMAT_DEEPSEEK; }
+            else if (value == "none") {     params.reasoning_format = COMMON_REASONING_FORMAT_NONE; }
+            else { std::invalid_argument("invalid value"); }
+        }
+    ).set_examples({LLAMA_EXAMPLE_SERVER, LLAMA_EXAMPLE_MAIN}).set_env("LLAMA_ARG_THINK"));
     add_opt(common_arg(
         {"--chat-template"}, "JINJA_TEMPLATE",
         string_format(
diff --git a/common/chat.cpp b/common/chat.cpp
index ef1c6fb3d..cf81c74b0 100644
--- a/common/chat.cpp
+++ b/common/chat.cpp
@@ -12,11 +12,13 @@ std::string common_chat_format_name(common_chat_format format) {
         case COMMON_CHAT_FORMAT_LLAMA_3_X: return "Llama 3.x";
         case COMMON_CHAT_FORMAT_LLAMA_3_X_WITH_BUILTIN_TOOLS: return "Llama 3.x with builtin tools";
         case COMMON_CHAT_FORMAT_DEEPSEEK_R1: return "DeepSeek R1";
+        case COMMON_CHAT_FORMAT_DEEPSEEK_R1_EXTRACT_REASONING: return "DeepSeek R1 (extract reasoning)";
         case COMMON_CHAT_FORMAT_FIREFUNCTION_V2: return "FireFunction v2";
         case COMMON_CHAT_FORMAT_FUNCTIONARY_V3_2: return "Functionary v3.2";
         case COMMON_CHAT_FORMAT_FUNCTIONARY_V3_1_LLAMA_3_1: return "Functionary v3.1 Llama 3.1";
         case COMMON_CHAT_FORMAT_HERMES_2_PRO: return "Hermes 2 Pro";
         case COMMON_CHAT_FORMAT_COMMAND_R7B: return "Command R7B";
+        case COMMON_CHAT_FORMAT_COMMAND_R7B_EXTRACT_REASONING: return "Command R7B (extract reasoning)";
         default:
             throw std::runtime_error("Unknown chat format");
     }
@@ -105,7 +107,6 @@ static common_chat_msg parse_json_tool_calls(
         std::sregex_iterator rend;
         std::sregex_iterator rit(it, end, function_regex);
         if (rit == rend) {
-            fprintf(stderr, "No more tool calls found\n");
             result.content += std::string(it, end);
             break;
         }
@@ -115,14 +116,21 @@ static common_chat_msg parse_json_tool_calls(
 
         json arguments;
         if (!parse_json(it, end, arguments)) {
-            throw std::runtime_error("Failed to parse json tool call arguments");
+            throw std::runtime_error("Failed to parse json tool call arguments: " + input);
         }
         if (!std::regex_search(it, end, match, close_regex)) {
-            throw std::runtime_error("Malformed input, missing closing pattern");
+            throw std::runtime_error("Malformed input, missing closing pattern: " + input);
         }
         it = match.suffix().first;
         result.tool_calls.push_back({name, arguments.is_string() ? arguments.get<std::string>() : arguments.dump(), /* id= */ ""});
     }
+
+    if (!result.tool_calls.empty()) {
+        if (!string_strip(result.content).empty()) {
+            LOG_WRN("Content found with tool calls: %s", result.content.c_str());
+        }
+        result.content = "";
+    }
     return result;
 }
 
@@ -382,22 +390,46 @@ static common_chat_params common_chat_params_init_command_r7b(const common_chat_
         "<|END_THINKING|>",
         "<|END_ACTION|>",
     };
-    data.prompt = apply(tmpl, inputs.messages, inputs.tools.empty() ? json() : inputs.tools, inputs.add_generation_prompt);
-    data.format = COMMON_CHAT_FORMAT_COMMAND_R7B;
+    auto adjusted_messages = json::array();
+    for (const auto & msg : inputs.messages) {
+        auto has_reasoning_content = msg.contains("reasoning_content") && msg["reasoning_content"].is_string();
+        auto has_tool_calls = msg.contains("tool_calls") && msg["tool_calls"].is_array();
+        if (has_reasoning_content && has_tool_calls) {
+            auto adjusted_message = msg;
+            adjusted_message["tool_plan"] = msg["reasoning_content"];
+            adjusted_message.erase("reasoning_content");
+            adjusted_messages.push_back(adjusted_message);
+        } else {
+            adjusted_messages.push_back(msg);
+        }
+    }
+    data.prompt = apply(tmpl, adjusted_messages, inputs.tools.empty() ? json() : inputs.tools, inputs.add_generation_prompt, {});
+    data.format = inputs.extract_reasoning ? COMMON_CHAT_FORMAT_COMMAND_R7B_EXTRACT_REASONING : COMMON_CHAT_FORMAT_COMMAND_R7B;
     return data;
 }
-static common_chat_msg common_chat_parse_command_r7b(const std::string & input) {
-    static std::regex response_regex("<\\|START_RESPONSE\\|>([\\s\\S\\n\\r]*?)<\\|END_RESPONSE\\|>");
-    static std::regex thought_action_regex("<\\|START_THINKING\\|>([\\s\\S\\n\\r]*?)<\\|END_THINKING\\|><\\|START_ACTION\\|>([\\s\\S\\n\\r]*?)<\\|END_ACTION\\|>");
+static common_chat_msg common_chat_parse_command_r7b(const std::string & input, bool extract_reasoning) {
+    static std::regex thought_regex("(<\\|START_THINKING\\|>([\\s\\S\\n\\r]*?)<\\|END_THINKING\\|>)([\\s\\S\\n\\r]*)");
+    static std::regex action_regex("<\\|START_ACTION\\|>([\\s\\S\\n\\r]*?)<\\|END_ACTION\\|>");
+    static std::regex response_regex("(?:<\\|START_RESPONSE\\|>)?([\\s\\S\\n\\r]*?)<\\|END_RESPONSE\\|>");
+
     std::smatch match;
 
     common_chat_msg result;
     result.role = "assistant";
-    if (std::regex_match(input, match, response_regex)) {
-        result.content = match[1].str();
-    } else if (std::regex_match(input, match, thought_action_regex)) {
-        result.tool_plan = match[1].str();
-        auto actions_str = match[2].str();
+
+    std::string rest = input;
+
+    if (std::regex_match(rest, match, thought_regex)) {
+        if (extract_reasoning) {
+            result.reasoning_content = match[2].str();
+        } else if (!match[2].str().empty()) {
+            // Let the unparsed thinking tags through in content only if their insides aren't empty.
+            result.content = match[1].str();
+        }
+        rest = match[3].str();
+    }
+    if (std::regex_match(rest, match, action_regex)) {
+        auto actions_str = match[1].str();
         auto actions = json::parse(actions_str);
         for (const auto & action : actions) {
             result.tool_calls.push_back({
@@ -406,9 +438,11 @@ static common_chat_msg common_chat_parse_command_r7b(const std::string & input)
                 /* .id = */        action["tool_call_id"],
             });
         }
+    } else if (std::regex_match(rest, match, response_regex)) {
+        auto response = match[1].str();
+        result.content += response;
     } else {
-        LOG_ERR("Failed to parse command_r output");
-        result.content = input;
+        result.content += rest;
     }
     return result;
 }
@@ -546,34 +580,90 @@ static common_chat_msg common_chat_parse_llama_3_1(const std::string & input, bo
 
 static common_chat_params common_chat_params_init_deepseek_r1(const common_chat_template & tmpl, const struct common_chat_inputs & inputs) {
     common_chat_params data;
-    data.grammar_lazy = inputs.tool_choice != "required";
-    data.grammar = build_grammar([&](const common_grammar_builder & builder) {
-        std::vector<std::string> tool_rules;
-        foreach_function(inputs.tools, [&](const json & tool) {
-            const auto & function = tool["function"];
-            std::string name = function["name"];
-            auto parameters = function["parameters"];
-            auto args_rule = builder.add_schema(name + "-args", parameters);
-            tool_rules.push_back(builder.add_rule(name + "-call",
-                "\"<｜tool▁call▁begin｜>function<｜tool▁sep｜>" + name + "\\n```json\\n\" " + args_rule + " \"```<｜tool▁call▁end｜>\""));
-        });
-        data.grammar_triggers.push_back({"<｜tool▁calls▁begin｜>", /* .at_start = */ false});
-        data.preserved_tokens = {
-            "<｜tool▁sep｜>",
-            "<｜tool▁call▁end｜>",
-        };
-        builder.add_rule("root", "\"<｜tool▁calls▁begin｜>\" (" + string_join(tool_rules, " | ") + ")" + (inputs.parallel_tool_calls ? "*" : "") + " space");
-    }, grammar_options);
+    if (inputs.tools.is_array() && !inputs.tools.empty()) {
+        data.grammar_lazy = inputs.tool_choice != "required" && inputs.json_schema.is_null();
+        data.grammar = build_grammar([&](const common_grammar_builder & builder) {
+            std::vector<std::string> tool_rules;
+            foreach_function(inputs.tools, [&](const json & tool) {
+                const auto & function = tool["function"];
+                std::string name = function["name"];
+                auto parameters = function["parameters"];
+                auto args_rule = builder.add_schema(name + "-args", parameters);
+                tool_rules.push_back(builder.add_rule(name + "-call",
+                    "\"<｜tool▁call▁begin｜>function<｜tool▁sep｜>" + name + "\\n"
+                    "```json\\n\" " + args_rule + " \"```<｜tool▁call▁end｜>\""));
+            });
+            // Distill Qwen 7B & 32B models seem confused re/ syntax of their tool call opening tag,
+            // so we accept common variants (then it's all constrained)
+            builder.add_rule("root",
+                "( \"<｜tool▁calls▁begin｜>\" | \"<｜tool_calls_begin｜>\" | \"<｜tool calls begin｜>\" | \"<｜tool\\\\_calls\\\\_begin｜>\" ) "
+                "(" + string_join(tool_rules, " | ") + ")" + (inputs.parallel_tool_calls ? "*" : "") + " "
+                "\"<｜tool▁calls▁end｜>\""
+                " space");
+            data.grammar_triggers.push_back({"<｜tool▁calls▁begin｜>", /* .at_start = */ false});
+            data.grammar_triggers.push_back({"<｜tool_calls_begin｜>", /* .at_start = */ false});
+            data.grammar_triggers.push_back({"<｜tool calls begin｜>", /* .at_start = */ false});
+            data.grammar_triggers.push_back({"<｜tool\\_calls\\_begin｜>", /* .at_start = */ false});
+            data.preserved_tokens = {
+                "<think>",
+                "</think>",
+                "<｜tool▁sep｜>",
+                "<｜tool▁calls▁end｜",
+                "<｜tool▁call▁end｜>",
+            };
+        }, grammar_options);
+    }
     auto prompt = apply(tmpl, inputs.messages, inputs.tools.empty() ? json() : inputs.tools, inputs.add_generation_prompt);
+
+    // Hacks to fix the official (broken) prompt.
+    // It is advisable to use --chat-template-file models/templates/llama-cpp-deepseek-r1.jinja instead,
+    // until the official template is fixed.
+    if (tmpl.source().find("{% if ns.is_tool %}{{'<｜tool▁outputs▁end｜>'}}") != std::string::npos) {
+        // Don't leave the chat dangling after tool results
+        if (string_ends_with(prompt, "<｜tool▁outputs▁end｜>")) {
+            prompt += "<｜end▁of▁sentence｜>";
+            if (inputs.add_generation_prompt) {
+                prompt += "<｜Assistant｜>";
+            }
+        }
+        // Fix up tool call delta example added by Minja
+        prompt = std::regex_replace(
+            prompt,
+            std::regex("(<｜tool▁call▁end｜>)[\\s\\r\\n]*(<｜tool▁outputs▁begin｜>|<｜User｜>)"),
+            "$1<｜tool▁calls▁end｜><｜end▁of▁sentence｜>$2");
+    }
     data.prompt = prompt;
-    data.format = COMMON_CHAT_FORMAT_DEEPSEEK_R1;
+    data.format = inputs.extract_reasoning ? COMMON_CHAT_FORMAT_DEEPSEEK_R1_EXTRACT_REASONING : COMMON_CHAT_FORMAT_DEEPSEEK_R1;
     return data;
 }
-static common_chat_msg common_chat_parse_deepseek_r1(const std::string & input) {
-    static std::regex trigger_regex("<｜tool▁calls▁begin｜>");
+static common_chat_msg common_chat_parse_deepseek_r1(const std::string & input, bool extract_reasoning) {
     static std::regex function_regex("<｜tool▁call▁begin｜>function<｜tool▁sep｜>([^\n]+)\n```json\n");
-    static std::regex close_regex("```<｜tool▁call▁end｜>");
-    return parse_json_tool_calls(input, trigger_regex, function_regex, close_regex);
+    static std::regex close_regex("```[\\s\\r\\n]*<｜tool▁call▁end｜>");
+    static std::regex reasoning_content_regex("((?:<think>)?([\\s\\S\\r\\n]*?)</think>)?([\\s\\S\\r\\n]*)");
+    static std::regex tool_calls_regex("[\\s\\r\\n]*(?:<｜tool▁calls▁begin｜>|<｜tool_calls_begin｜>|<｜tool calls begin｜>|<｜tool\\\\_calls\\\\_begin｜>)([\\s\\S\\r\\n]*?)<｜tool▁calls▁end｜>");
+    common_chat_msg msg;
+    msg.role = "assistant";
+    std::smatch match;
+    if (std::regex_match(input, match, reasoning_content_regex)) {
+        std::string rest;
+        if (extract_reasoning) {
+            msg.reasoning_content = string_strip(match[2].str());
+        } else {
+            msg.content = match[1].str();
+        }
+        rest = match[3].str();
+
+        if (std::regex_search(rest, match, tool_calls_regex)) {
+            auto tool_calls = match[1].str();
+            auto msg2 = parse_json_tool_calls(tool_calls, std::nullopt, function_regex, close_regex);
+            msg.tool_calls = std::move(msg2.tool_calls);
+        } else {
+            msg.content += std::string(rest.begin() + rest.find_first_not_of(" \r\n"), rest.end());
+        }
+    } else {
+        msg.content = input;
+    }
+    return msg;
 }
 
 static common_chat_params common_chat_params_init_firefunction_v2(const common_chat_template & tmpl, const struct common_chat_inputs & inputs) {
@@ -583,7 +673,7 @@ static common_chat_params common_chat_params_init_firefunction_v2(const common_c
         {"datetime", "Jan 29 2025 13:00:00 GMT"},
         {"functions", json(inputs.tools.empty() ? "" : inputs.tools.dump(2))},
     });
-    if (!inputs.tools.is_null() && !inputs.tools.empty()) {
+    if (inputs.tools.is_array() && !inputs.tools.empty()) {
         data.grammar_lazy = inputs.tool_choice != "required";
         data.grammar = build_grammar([&](const common_grammar_builder & builder) {
             auto schemas = json::array();
@@ -628,7 +718,7 @@ static common_chat_params common_chat_params_init_functionary_v3_2(const common_
     common_chat_params data;
     data.prompt = apply(tmpl, inputs.messages, inputs.tools.empty() ? json() : inputs.tools, inputs.add_generation_prompt);
     data.format = COMMON_CHAT_FORMAT_FUNCTIONARY_V3_2;
-    if (!inputs.tools.is_null() && !inputs.tools.empty()) {
+    if (inputs.tools.is_array() && !inputs.tools.empty()) {
         data.grammar_lazy = inputs.tool_choice != "required";
         data.grammar = build_grammar([&](const common_grammar_builder & builder) {
             std::vector<std::string> first_tool_rules;
@@ -884,47 +974,72 @@ static common_chat_params common_chat_params_init_without_tools(const common_cha
 }
 
 common_chat_params common_chat_params_init(const common_chat_template & tmpl, const struct common_chat_inputs & inputs) {
-    auto has_tools = !inputs.tools.is_null() && inputs.tool_choice != "none";
-    LOG_DBG("[%s] has_tools=%s\n", __func__, has_tools ? "true" : "false");
+    const auto & src = tmpl.source();
+    const auto & caps = tmpl.original_caps();
 
-    if (has_tools && !inputs.grammar.empty()) {
-        throw std::runtime_error("Cannot specify grammar with tools");
+    if (inputs.tools.is_array()) {
+        if (inputs.tool_choice != "none" && !inputs.grammar.empty()) {
+            throw std::runtime_error("Cannot specify grammar with tools");
+        }
+        if (caps.supports_tool_calls && !caps.supports_tools) {
+            LOG_WRN("Template supports tool calls but does not natively describe tools. The fallback behaviour used may produce bad results, inspect prompt w/ --verbose & consider overriding the template.");
+        }
     }
 
-    const auto & src = tmpl.source();
+    // DeepSeek R1: use handler in all cases except json schema (thinking / tools).
+    if (src.find("<｜tool▁calls▁begin｜>") != std::string::npos && inputs.json_schema.is_null()) {
+        return common_chat_params_init_deepseek_r1(tmpl, inputs);
+    }
+
+    // Command R7B: : use handler in all cases except json schema (thinking / tools).
+    if (src.find("<|END_THINKING|><|START_ACTION|>") != std::string::npos && inputs.json_schema.is_null()) {
+        return common_chat_params_init_command_r7b(tmpl, inputs);
+    }
+
+    // Use generic handler when mixing tools + JSON schema.
+    // TODO: support that mix in handlers below.
+    if ((!inputs.tools.is_array() && inputs.json_schema.is_object())) {
+        return common_chat_params_init_generic(tmpl, inputs);
+    }
+
+    // Functionary prepends "all\n" to plain content outputs, so we use its handler in all cases.
     if (src.find(">>>all") != std::string::npos) {
-        // Functionary prepends "all\n" to plain content outputs, so we use the parser no matter when
         return common_chat_params_init_functionary_v3_2(tmpl, inputs);
     }
+
+    // Firefunction v2 requires datetime and functions in the context even w/o tools, so we also use its handler in all cases.
     if (src.find(" functools[") != std::string::npos) {
-        // Firefunction v2 requires datetime and functions in the context, even w/o tools.
         return common_chat_params_init_firefunction_v2(tmpl, inputs);
     }
 
-    if (!has_tools) {
+    // Plain handler (no tools)
+    if (inputs.tools.is_null() || inputs.tool_choice == "none") {
         return common_chat_params_init_without_tools(tmpl, inputs);
     }
 
+    // Hermes 2/3 Pro, Qwen 2.5 Instruct (w/ tools)
     if (src.find("<tool_call>") != std::string::npos) {
         return common_chat_params_init_hermes_2_pro(tmpl, inputs);
     }
+
+    // Functionary v3.1 (w/ tools)
     if (src.find("<|start_header_id|>") != std::string::npos
         && src.find("<function=") != std::string::npos) {
         return common_chat_params_init_functionary_v3_1_llama_3_1(tmpl, inputs);
     }
+
+    // Llama 3.1, 3.2, 3.3 (w/ tools)
     if (src.find("<|start_header_id|>ipython<|end_header_id|>") != std::string::npos) {
         auto allow_python_tag_builtin_tools = src.find("<|python_tag|>") != std::string::npos;
         return common_chat_params_init_llama_3_1_tool_calls(tmpl, inputs, allow_python_tag_builtin_tools);
     }
-    if (src.find("<｜tool▁calls▁begin｜>") != std::string::npos) {
-        return common_chat_params_init_deepseek_r1(tmpl, inputs);
-    }
+
+    // Mistral Nemo (w/ tools)
     if (src.find("[TOOL_CALLS]") != std::string::npos) {
         return common_chat_params_init_mistral_nemo(tmpl, inputs);
     }
-    if (src.find("<|END_THINKING|><|START_ACTION|>") != std::string::npos) {
-        return common_chat_params_init_command_r7b(tmpl, inputs);
-    }
+
+    // Generic fallback
     return common_chat_params_init_generic(tmpl, inputs);
 }
 
@@ -949,7 +1064,9 @@ common_chat_msg common_chat_parse(const std::string & input, common_chat_format
         case COMMON_CHAT_FORMAT_LLAMA_3_X_WITH_BUILTIN_TOOLS:
             return common_chat_parse_llama_3_1(input, /* with_builtin_tools= */ true);
         case COMMON_CHAT_FORMAT_DEEPSEEK_R1:
-            return common_chat_parse_deepseek_r1(input);
+            return common_chat_parse_deepseek_r1(input, /* extract_reasoning= */ false);
+        case COMMON_CHAT_FORMAT_DEEPSEEK_R1_EXTRACT_REASONING:
+            return common_chat_parse_deepseek_r1(input, /* extract_reasoning= */ true);
         case COMMON_CHAT_FORMAT_FUNCTIONARY_V3_2:
             return common_chat_parse_functionary_v3_2(input);
         case COMMON_CHAT_FORMAT_FUNCTIONARY_V3_1_LLAMA_3_1:
@@ -959,7 +1076,9 @@ common_chat_msg common_chat_parse(const std::string & input, common_chat_format
         case COMMON_CHAT_FORMAT_FIREFUNCTION_V2:
             return common_chat_parse_firefunction_v2(input);
         case COMMON_CHAT_FORMAT_COMMAND_R7B:
-            return common_chat_parse_command_r7b(input);
+            return common_chat_parse_command_r7b(input, /* extract_reasoning= */ false);
+        case COMMON_CHAT_FORMAT_COMMAND_R7B_EXTRACT_REASONING:
+            return common_chat_parse_command_r7b(input, /* extract_reasoning= */ true);
         default:
             throw std::runtime_error("Unsupported format: " + common_chat_format_name(format));
     }
diff --git a/common/chat.hpp b/common/chat.hpp
index 33e64a430..ba1632f66 100644
--- a/common/chat.hpp
+++ b/common/chat.hpp
@@ -19,6 +19,7 @@ struct common_chat_inputs {
     bool stream;
     std::string grammar;
     bool add_generation_prompt = true;
+    bool extract_reasoning     = true;
 };
 
 enum common_chat_format {
@@ -28,11 +29,13 @@ enum common_chat_format {
     COMMON_CHAT_FORMAT_LLAMA_3_X,
     COMMON_CHAT_FORMAT_LLAMA_3_X_WITH_BUILTIN_TOOLS,
     COMMON_CHAT_FORMAT_DEEPSEEK_R1,
+    COMMON_CHAT_FORMAT_DEEPSEEK_R1_EXTRACT_REASONING,
     COMMON_CHAT_FORMAT_FIREFUNCTION_V2,
     COMMON_CHAT_FORMAT_FUNCTIONARY_V3_2,
     COMMON_CHAT_FORMAT_FUNCTIONARY_V3_1_LLAMA_3_1,
     COMMON_CHAT_FORMAT_HERMES_2_PRO,
     COMMON_CHAT_FORMAT_COMMAND_R7B,
+    COMMON_CHAT_FORMAT_COMMAND_R7B_EXTRACT_REASONING,
 
     COMMON_CHAT_FORMAT_COUNT, // Not a format, just the # formats
 };
diff --git a/common/common.h b/common/common.h
index b208d0c7e..3c5b4910b 100644
--- a/common/common.h
+++ b/common/common.h
@@ -202,6 +202,11 @@ struct common_params_vocoder {
     bool use_guide_tokens = false; // enable guide tokens to improve TTS accuracy            // NOLINT
 };
 
+enum common_reasoning_format {
+    COMMON_REASONING_FORMAT_NONE,
+    COMMON_REASONING_FORMAT_DEEPSEEK, // Extract thinking tag contents and return as `message.reasoning_content`
+};
+
 struct common_params {
     int32_t n_predict             =    -1; // new tokens to predict
     int32_t n_ctx                 =  4096; // context size
@@ -346,6 +351,7 @@ struct common_params {
     std::string chat_template = "";                                                                         // NOLINT
     bool use_jinja = false;                                                                                 // NOLINT
     bool enable_chat_template = true;
+    common_reasoning_format reasoning_format = COMMON_REASONING_FORMAT_DEEPSEEK;
 
     std::vector<std::string> api_keys;
 
@@ -623,7 +629,7 @@ struct common_chat_msg {
     std::string role;
     std::string content;
     std::vector<common_tool_call> tool_calls;
-    std::string tool_plan = "";
+    std::string reasoning_content = "";
 };
 
 // Check if the template supplied via "--chat-template" is supported or not. Returns true if it's valid
diff --git a/common/sampling.cpp b/common/sampling.cpp
index e4b21ca10..1ca26f1e3 100644
--- a/common/sampling.cpp
+++ b/common/sampling.cpp
@@ -151,12 +151,6 @@ struct common_sampler * common_sampler_init(const struct llama_model * model, co
 
     lparams.no_perf = params.no_perf;
 
-    std::vector<const char *> trigger_words;
-    trigger_words.reserve(params.grammar_trigger_words.size());
-    for (const auto & str : params.grammar_trigger_words) {
-        trigger_words.push_back(str.word.c_str());
-    }
-
     struct llama_sampler * grmr;
     if (params.grammar.compare(0, 11, "%llguidance") == 0) {
 #ifdef LLAMA_USE_LLGUIDANCE
@@ -165,6 +159,12 @@ struct common_sampler * common_sampler_init(const struct llama_model * model, co
         GGML_ABORT("llguidance (cmake -DLLAMA_LLGUIDANCE=ON) is not enabled");
 #endif // LLAMA_USE_LLGUIDANCE
     } else {
+        std::vector<const char *> trigger_words;
+        trigger_words.reserve(params.grammar_trigger_words.size());
+        for (const auto & str : params.grammar_trigger_words) {
+            trigger_words.push_back(str.word.c_str());
+        }
+
         grmr = params.grammar_lazy
              ? llama_sampler_init_grammar_lazy(vocab, params.grammar.c_str(), "root",
                                                trigger_words.data(), trigger_words.size(),
diff --git a/examples/server/README.md b/examples/server/README.md
index d0b262f0e..1e726fdd5 100644
--- a/examples/server/README.md
+++ b/examples/server/README.md
@@ -127,6 +127,7 @@ The project is under active development, and we are [looking for feedback and co
 | `--grammar-file FNAME` | file to read grammar from |
 | `-j, --json-schema SCHEMA` | JSON schema to constrain generations (https://json-schema.org/), e.g. `{}` for any JSON object<br/>For schemas w/ external $refs, use --grammar + example/json_schema_to_grammar.py instead |
 | `--jinja` | Enable experimental Jinja templating engine (required for tool use) |
+| `--reasoning-format FORMAT` | Controls extraction of model thinking traces and the format / field in which they are returned (default: `deepseek`; allowed values: `deepseek`, `none`; requires `--jinja`). `none` will leave thinking traces inline in `message.content` in a model-specific format, while `deepseek` will return them separately under `message.reasoning_content` |
 
 **Example-specific params**
 
@@ -1136,61 +1137,252 @@ curl http://localhost:8080/v1/chat/completions \
 
   | Template | Format |
   |----------|--------|
-  | CohereForAI-c4ai-command-r-plus-default.jinja | generic tool calls |
-  | CohereForAI-c4ai-command-r-plus-rag.jinja | generic tool calls |
-  | CohereForAI-c4ai-command-r-plus-tool_use.jinja | generic tool calls |
-  | MiniMaxAI-MiniMax-Text-01.jinja | generic tool calls |
-  | NexaAIDev-Octopus-v2.jinja | generic tool calls |
-  | NousResearch-Hermes-2-Pro-Llama-3-8B-default.jinja | generic tool calls |
-  | NousResearch-Hermes-2-Pro-Llama-3-8B-tool_use.jinja | hermes 2 pro tool calls |
-  | NousResearch-Hermes-2-Pro-Mistral-7B-default.jinja | generic tool calls |
-  | NousResearch-Hermes-2-Pro-Mistral-7B-tool_use.jinja | hermes 2 pro tool calls |
-  | NousResearch-Hermes-3-Llama-3.1-70B-default.jinja | generic tool calls |
-  | NousResearch-Hermes-3-Llama-3.1-70B-tool_use.jinja | hermes 2 pro tool calls |
-  | OrionStarAI-Orion-14B-Chat.jinja | generic tool calls |
-  | Qwen-QwQ-32B-Preview.jinja | hermes 2 pro tool calls |
-  | Qwen-Qwen2-7B-Instruct.jinja | generic tool calls |
-  | Qwen-Qwen2-VL-7B-Instruct.jinja | generic tool calls |
-  | Qwen-Qwen2.5-7B-Instruct.jinja | hermes 2 pro tool calls |
-  | Qwen-Qwen2.5-Math-7B-Instruct.jinja | hermes 2 pro tool calls |
-  | TheBloke-FusionNet_34Bx2_MoE-AWQ.jinja | generic tool calls |
-  | abacusai-Fewshot-Metamath-OrcaVicuna-Mistral.jinja | generic tool calls |
-  | bofenghuang-vigogne-2-70b-chat.jinja | generic tool calls |
-  | databricks-dbrx-instruct.jinja | generic tool calls |
-  | deepseek-ai-DeepSeek-Coder-V2-Instruct.jinja | generic tool calls |
-  | deepseek-ai-DeepSeek-R1-Distill-Llama-8B.jinja | deepseek r1 tool calls |
-  | deepseek-ai-DeepSeek-R1-Distill-Qwen-32B.jinja | deepseek r1 tool calls |
-  | deepseek-ai-DeepSeek-R1-Distill-Qwen-7B.jinja | deepseek r1 tool calls |
-  | deepseek-ai-DeepSeek-V2.5.jinja | deepseek r1 tool calls |
-  | deepseek-ai-deepseek-coder-33b-instruct.jinja | generic tool calls |
-  | google-gemma-2-2b-it.jinja | generic tool calls |
-  | google-gemma-7b-it.jinja | generic tool calls |
-  | indischepartij-MiniCPM-3B-OpenHermes-2.5-v2.jinja | generic tool calls |
-  | mattshumer-Reflection-Llama-3.1-70B.jinja | generic tool calls |
-  | meetkai-functionary-medium-v3.2.jinja | functionary v3.2 tool calls |
-  | meta-llama-Llama-3.1-8B-Instruct.jinja | llama 3.x tool calls (w/ builtin tools) |
-  | meta-llama-Llama-3.2-3B-Instruct.jinja | llama 3.x tool calls |
-  | meta-llama-Llama-3.3-70B-Instruct.jinja | llama 3.x tool calls (w/ builtin tools) |
-  | meta-llama-Meta-Llama-3.1-8B-Instruct.jinja | llama 3.x tool calls (w/ builtin tools) |
-  | microsoft-Phi-3-medium-4k-instruct.jinja | generic tool calls |
-  | microsoft-Phi-3-mini-4k-instruct.jinja | generic tool calls |
-  | microsoft-Phi-3-small-8k-instruct.jinja | generic tool calls |
-  | microsoft-Phi-3.5-mini-instruct.jinja | generic tool calls |
-  | microsoft-Phi-3.5-vision-instruct.jinja | generic tool calls |
-  | mistralai-Mistral-7B-Instruct-v0.2.jinja | generic tool calls |
-  | mistralai-Mistral-Large-Instruct-2407.jinja | mistral nemo tool calls |
-  | mistralai-Mistral-Large-Instruct-2411.jinja | generic tool calls |
-  | mistralai-Mistral-Nemo-Instruct-2407.jinja | mistral nemo tool calls |
-  | mistralai-Mixtral-8x7B-Instruct-v0.1.jinja | generic tool calls |
-  | mlabonne-AlphaMonarch-7B.jinja | generic tool calls |
-  | nvidia-Llama-3.1-Nemotron-70B-Instruct-HF.jinja | llama 3.x tool calls (w/ builtin tools) |
-  | openchat-openchat-3.5-0106.jinja | generic tool calls |
-  | teknium-OpenHermes-2.5-Mistral-7B.jinja | generic tool calls |
+  | Almawave-Velvet-14B.jinja | Hermes 2 Pro |
+  | AtlaAI-Selene-1-Mini-Llama-3.1-8B.jinja | Llama 3.x |
+  | CohereForAI-aya-expanse-8b.jinja | Generic |
+  | CohereForAI-c4ai-command-r-plus-default.jinja | Generic |
+  | CohereForAI-c4ai-command-r-plus-rag.jinja | Generic |
+  | CohereForAI-c4ai-command-r-plus-tool_use.jinja | Generic |
+  | CohereForAI-c4ai-command-r7b-12-2024-default.jinja | Command R7B (extract reasoning) |
+  | CohereForAI-c4ai-command-r7b-12-2024-rag.jinja | Command R7B (extract reasoning) |
+  | CohereForAI-c4ai-command-r7b-12-2024-tool_use.jinja | Command R7B (extract reasoning) |
+  | CohereForAI-c4ai-command-r7b-12-2024.jinja | Generic |
+  | DavieLion-Llama-3.2-1B-SPIN-iter3.jinja | Generic |
+  | Delta-Vector-Rei-12B.jinja | Mistral Nemo |
+  | EpistemeAI-Mistral-Nemo-Instruct-12B-Philosophy-Math.jinja | Mistral Nemo |
+  | FlofloB-83k_continued_pretraining_Qwen2.5-0.5B-Instruct_Unsloth_merged_16bit.jinja | Hermes 2 Pro |
+  | FlofloB-test_continued_pretraining_Phi-3-mini-4k-instruct_Unsloth_merged_16bit.jinja | Generic |
+  | HelpingAI-HAI-SER.jinja | Generic |
+  | HuggingFaceTB-SmolLM2-1.7B-Instruct.jinja | Generic |
+  | HuggingFaceTB-SmolLM2-135M-Instruct.jinja | Generic |
+  | HuggingFaceTB-SmolLM2-360M-Instruct.jinja | Generic |
+  | INSAIT-Institute-BgGPT-Gemma-2-27B-IT-v1.0.jinja | Generic |
+  | Ihor-Text2Graph-R1-Qwen2.5-0.5b.jinja | Hermes 2 Pro |
+  | Infinigence-Megrez-3B-Instruct.jinja | Generic |
+  | Josephgflowers-TinyLlama_v1.1_math_code-world-test-1.jinja | Generic |
+  | LGAI-EXAONE-EXAONE-3.5-2.4B-Instruct.jinja | Generic |
+  | LGAI-EXAONE-EXAONE-3.5-7.8B-Instruct.jinja | Generic |
+  | LatitudeGames-Wayfarer-12B.jinja | Generic |
+  | Magpie-Align-Llama-3-8B-Magpie-Align-v0.1.jinja | Generic |
+  | Magpie-Align-Llama-3.1-8B-Magpie-Align-v0.1.jinja | Generic |
+  | MaziyarPanahi-calme-3.2-instruct-78b.jinja | Generic |
+  | MiniMaxAI-MiniMax-Text-01.jinja | Generic |
+  | MiniMaxAI-MiniMax-VL-01.jinja | Generic |
+  | NaniDAO-deepseek-r1-qwen-2.5-32B-ablated.jinja | DeepSeek R1 (extract reasoning) |
+  | NexaAIDev-Octopus-v2.jinja | Generic |
+  | NousResearch-Hermes-2-Pro-Llama-3-8B-default.jinja | Generic |
+  | NousResearch-Hermes-2-Pro-Llama-3-8B-tool_use.jinja | Hermes 2 Pro |
+  | NousResearch-Hermes-2-Pro-Mistral-7B-default.jinja | Generic |
+  | NousResearch-Hermes-2-Pro-Mistral-7B-tool_use.jinja | Hermes 2 Pro |
+  | NousResearch-Hermes-3-Llama-3.1-70B-default.jinja | Generic |
+  | NousResearch-Hermes-3-Llama-3.1-70B-tool_use.jinja | Hermes 2 Pro |
+  | NovaSky-AI-Sky-T1-32B-Flash.jinja | Hermes 2 Pro |
+  | NovaSky-AI-Sky-T1-32B-Preview.jinja | Hermes 2 Pro |
+  | OnlyCheeini-greesychat-turbo.jinja | Generic |
+  | Orenguteng-Llama-3.1-8B-Lexi-Uncensored-V2.jinja | Llama 3.x |
+  | OrionStarAI-Orion-14B-Chat.jinja | Generic |
+  | PowerInfer-SmallThinker-3B-Preview.jinja | Generic |
+  | PrimeIntellect-INTELLECT-1-Instruct.jinja | Generic |
+  | Qwen-QVQ-72B-Preview.jinja | Generic |
+  | Qwen-QwQ-32B-Preview.jinja | Hermes 2 Pro |
+  | Qwen-Qwen1.5-7B-Chat.jinja | Generic |
+  | Qwen-Qwen2-7B-Instruct.jinja | Generic |
+  | Qwen-Qwen2-VL-72B-Instruct.jinja | Generic |
+  | Qwen-Qwen2-VL-7B-Instruct.jinja | Generic |
+  | Qwen-Qwen2.5-0.5B.jinja | Hermes 2 Pro |
+  | Qwen-Qwen2.5-1.5B-Instruct.jinja | Hermes 2 Pro |
+  | Qwen-Qwen2.5-14B-Instruct-1M.jinja | Hermes 2 Pro |
+  | Qwen-Qwen2.5-14B.jinja | Hermes 2 Pro |
+  | Qwen-Qwen2.5-32B-Instruct.jinja | Hermes 2 Pro |
+  | Qwen-Qwen2.5-32B.jinja | Hermes 2 Pro |
+  | Qwen-Qwen2.5-3B-Instruct.jinja | Hermes 2 Pro |
+  | Qwen-Qwen2.5-72B-Instruct.jinja | Hermes 2 Pro |
+  | Qwen-Qwen2.5-7B-Instruct-1M.jinja | Hermes 2 Pro |
+  | Qwen-Qwen2.5-7B-Instruct.jinja | Hermes 2 Pro |
+  | Qwen-Qwen2.5-7B.jinja | Hermes 2 Pro |
+  | Qwen-Qwen2.5-Coder-32B-Instruct.jinja | Hermes 2 Pro |
+  | Qwen-Qwen2.5-Coder-7B-Instruct.jinja | Hermes 2 Pro |
+  | Qwen-Qwen2.5-Math-1.5B.jinja | Hermes 2 Pro |
+  | Qwen-Qwen2.5-Math-7B-Instruct.jinja | Hermes 2 Pro |
+  | Qwen-Qwen2.5-VL-3B-Instruct.jinja | Hermes 2 Pro |
+  | Qwen-Qwen2.5-VL-72B-Instruct.jinja | Hermes 2 Pro |
+  | Qwen-Qwen2.5-VL-7B-Instruct.jinja | Hermes 2 Pro |
+  | RWKV-Red-Team-ARWKV-7B-Preview-0.1.jinja | Hermes 2 Pro |
+  | SakanaAI-TinySwallow-1.5B-Instruct.jinja | Hermes 2 Pro |
+  | SakanaAI-TinySwallow-1.5B.jinja | Hermes 2 Pro |
+  | Sao10K-70B-L3.3-Cirrus-x1.jinja | Llama 3.x |
+  | SentientAGI-Dobby-Mini-Leashed-Llama-3.1-8B.jinja | Llama 3.x |
+  | SentientAGI-Dobby-Mini-Unhinged-Llama-3.1-8B.jinja | Llama 3.x |
+  | Steelskull-L3.3-Damascus-R1.jinja | Llama 3.x |
+  | Steelskull-L3.3-MS-Nevoria-70b.jinja | Llama 3.x |
+  | Steelskull-L3.3-Nevoria-R1-70b.jinja | Llama 3.x |
+  | THUDM-glm-4-9b-chat.jinja | Generic |
+  | THUDM-glm-edge-1.5b-chat.jinja | Generic |
+  | Tarek07-Progenitor-V1.1-LLaMa-70B.jinja | Llama 3.x |
+  | TheBloke-FusionNet_34Bx2_MoE-AWQ.jinja | Generic |
+  | TinyLlama-TinyLlama-1.1B-Chat-v1.0.jinja | Generic |
+  | UCLA-AGI-Mistral7B-PairRM-SPPO-Iter3.jinja | Generic |
+  | ValiantLabs-Llama3.1-8B-Enigma.jinja | Llama 3.x |
+  | abacusai-Fewshot-Metamath-OrcaVicuna-Mistral.jinja | Generic |
+  | ai21labs-AI21-Jamba-1.5-Large.jinja | Generic |
+  | allenai-Llama-3.1-Tulu-3-405B-SFT.jinja | Generic |
+  | allenai-Llama-3.1-Tulu-3-405B.jinja | Generic |
+  | allenai-Llama-3.1-Tulu-3-8B.jinja | Generic |
+  | arcee-ai-Virtuoso-Lite.jinja | Hermes 2 Pro |
+  | arcee-ai-Virtuoso-Medium-v2.jinja | Hermes 2 Pro |
+  | arcee-ai-Virtuoso-Small-v2.jinja | Hermes 2 Pro |
+  | avemio-GRAG-NEMO-12B-ORPO-HESSIAN-AI.jinja | Generic |
+  | bespokelabs-Bespoke-Stratos-7B.jinja | Hermes 2 Pro |
+  | bfuzzy1-acheron-m1a-llama.jinja | Generic |
+  | bofenghuang-vigogne-2-70b-chat.jinja | Generic |
+  | bytedance-research-UI-TARS-72B-DPO.jinja | Generic |
+  | bytedance-research-UI-TARS-7B-DPO.jinja | Generic |
+  | bytedance-research-UI-TARS-7B-SFT.jinja | Generic |
+  | carsenk-phi3.5_mini_exp_825_uncensored.jinja | Generic |
+  | cyberagent-DeepSeek-R1-Distill-Qwen-14B-Japanese.jinja | DeepSeek R1 (extract reasoning) |
+  | cyberagent-DeepSeek-R1-Distill-Qwen-32B-Japanese.jinja | DeepSeek R1 (extract reasoning) |
+  | databricks-dbrx-instruct.jinja | Generic |
+  | deepseek-ai-DeepSeek-Coder-V2-Instruct.jinja | Generic |
+  | deepseek-ai-DeepSeek-Coder-V2-Lite-Base.jinja | Generic |
+  | deepseek-ai-DeepSeek-Coder-V2-Lite-Instruct.jinja | Generic |
+  | deepseek-ai-DeepSeek-R1-Distill-Llama-70B.jinja | DeepSeek R1 (extract reasoning) |
+  | deepseek-ai-DeepSeek-R1-Distill-Llama-8B.jinja | DeepSeek R1 (extract reasoning) |
+  | deepseek-ai-DeepSeek-R1-Distill-Qwen-1.5B.jinja | DeepSeek R1 (extract reasoning) |
+  | deepseek-ai-DeepSeek-R1-Distill-Qwen-14B.jinja | DeepSeek R1 (extract reasoning) |
+  | deepseek-ai-DeepSeek-R1-Distill-Qwen-32B.jinja | DeepSeek R1 (extract reasoning) |
+  | deepseek-ai-DeepSeek-R1-Distill-Qwen-7B.jinja | DeepSeek R1 (extract reasoning) |
+  | deepseek-ai-DeepSeek-R1-Zero.jinja | DeepSeek R1 (extract reasoning) |
+  | deepseek-ai-DeepSeek-R1.jinja | DeepSeek R1 (extract reasoning) |
+  | deepseek-ai-DeepSeek-V2-Lite.jinja | Generic |
+  | deepseek-ai-DeepSeek-V2.5.jinja | DeepSeek R1 (extract reasoning) |
+  | deepseek-ai-DeepSeek-V3.jinja | DeepSeek R1 (extract reasoning) |
+  | deepseek-ai-deepseek-coder-33b-instruct.jinja | Generic |
+  | deepseek-ai-deepseek-coder-6.7b-instruct.jinja | Generic |
+  | deepseek-ai-deepseek-coder-7b-instruct-v1.5.jinja | Generic |
+  | deepseek-ai-deepseek-llm-67b-chat.jinja | Generic |
+  | deepseek-ai-deepseek-llm-7b-chat.jinja | Generic |
+  | dicta-il-dictalm2.0-instruct.jinja | Generic |
+  | ehristoforu-Falcon3-8B-Franken-Basestruct.jinja | Hermes 2 Pro |
+  | fireworks-ai-llama-3-firefunction-v2.jinja | FireFunction v2 |
+  | godlikehhd-alpaca_data_sampled_ifd_new_5200.jinja | Hermes 2 Pro |
+  | godlikehhd-alpaca_data_score_max_0.7_2600.jinja | Hermes 2 Pro |
+  | google-gemma-2-27b-it.jinja | Generic |
+  | google-gemma-2-2b-it.jinja | Generic |
+  | google-gemma-2-2b-jpn-it.jinja | Generic |
+  | google-gemma-7b-it.jinja | Generic |
+  | huihui-ai-DeepSeek-R1-Distill-Llama-70B-abliterated.jinja | DeepSeek R1 (extract reasoning) |
+  | huihui-ai-DeepSeek-R1-Distill-Llama-8B-abliterated.jinja | DeepSeek R1 (extract reasoning) |
+  | huihui-ai-DeepSeek-R1-Distill-Qwen-14B-abliterated-v2.jinja | DeepSeek R1 (extract reasoning) |
+  | huihui-ai-DeepSeek-R1-Distill-Qwen-32B-abliterated.jinja | DeepSeek R1 (extract reasoning) |
+  | huihui-ai-DeepSeek-R1-Distill-Qwen-7B-abliterated-v2.jinja | DeepSeek R1 (extract reasoning) |
+  | huihui-ai-Qwen2.5-14B-Instruct-1M-abliterated.jinja | Hermes 2 Pro |
+  | ibm-granite-granite-3.1-8b-instruct.jinja | Generic |
+  | indischepartij-MiniCPM-3B-OpenHermes-2.5-v2.jinja | Generic |
+  | inflatebot-MN-12B-Mag-Mell-R1.jinja | Generic |
+  | jinaai-ReaderLM-v2.jinja | Generic |
+  | kms7530-chemeng_qwen-math-7b_24_1_100_1_nonmath.jinja | Hermes 2 Pro |
+  | knifeayumu-Cydonia-v1.3-Magnum-v4-22B.jinja | Mistral Nemo |
+  | langgptai-qwen1.5-7b-chat-sa-v0.1.jinja | Generic |
+  | lightblue-DeepSeek-R1-Distill-Qwen-7B-Japanese.jinja | DeepSeek R1 (extract reasoning) |
+  | mattshumer-Reflection-Llama-3.1-70B.jinja | Generic |
+  | meetkai-functionary-medium-v3.1.jinja | Functionary v3.1 Llama 3.1 |
+  | meetkai-functionary-medium-v3.2.jinja | Functionary v3.2 |
+  | meta-llama-Llama-2-7b-chat-hf.jinja | Generic |
+  | meta-llama-Llama-3.1-8B-Instruct.jinja | Llama 3.x |
+  | meta-llama-Llama-3.2-11B-Vision-Instruct.jinja | Llama 3.x |
+  | meta-llama-Llama-3.2-1B-Instruct.jinja | Llama 3.x |
+  | meta-llama-Llama-3.2-3B-Instruct.jinja | Llama 3.x |
+  | meta-llama-Llama-3.3-70B-Instruct.jinja | Llama 3.x |
+  | meta-llama-Meta-Llama-3-8B-Instruct.jinja | Generic |
+  | meta-llama-Meta-Llama-3.1-8B-Instruct.jinja | Llama 3.x |
+  | microsoft-Phi-3-medium-4k-instruct.jinja | Generic |
+  | microsoft-Phi-3-mini-4k-instruct.jinja | Generic |
+  | microsoft-Phi-3-small-8k-instruct.jinja | Generic |
+  | microsoft-Phi-3.5-mini-instruct.jinja | Generic |
+  | microsoft-Phi-3.5-vision-instruct.jinja | Generic |
+  | microsoft-phi-4.jinja | Generic |
+  | migtissera-Tess-3-Mistral-Nemo-12B.jinja | Generic |
+  | ministral-Ministral-3b-instruct.jinja | Generic |
+  | mistralai-Codestral-22B-v0.1.jinja | Generic |
+  | mistralai-Mistral-7B-Instruct-v0.1.jinja | Generic |
+  | mistralai-Mistral-7B-Instruct-v0.2.jinja | Generic |
+  | mistralai-Mistral-7B-Instruct-v0.3.jinja | Mistral Nemo |
+  | mistralai-Mistral-Large-Instruct-2407.jinja | Mistral Nemo |
+  | mistralai-Mistral-Large-Instruct-2411.jinja | Generic |
+  | mistralai-Mistral-Nemo-Instruct-2407.jinja | Mistral Nemo |
+  | mistralai-Mistral-Small-24B-Instruct-2501.jinja | Generic |
+  | mistralai-Mixtral-8x7B-Instruct-v0.1.jinja | Generic |
+  | mkurman-Qwen2.5-14B-DeepSeek-R1-1M.jinja | Hermes 2 Pro |
+  | mlabonne-AlphaMonarch-7B.jinja | Generic |
+  | mlx-community-Josiefied-Qwen2.5-0.5B-Instruct-abliterated-v1-float32.jinja | Hermes 2 Pro |
+  | mlx-community-Qwen2.5-VL-7B-Instruct-8bit.jinja | Hermes 2 Pro |
+  | mobiuslabsgmbh-DeepSeek-R1-ReDistill-Qwen-1.5B-v1.1.jinja | DeepSeek R1 (extract reasoning) |
+  | netcat420-MFANNv0.20.jinja | Generic |
+  | netcat420-MFANNv0.24.jinja | Generic |
+  | netease-youdao-Confucius-o1-14B.jinja | Hermes 2 Pro |
+  | nvidia-AceMath-7B-RM.jinja | Hermes 2 Pro |
+  | nvidia-Eagle2-1B.jinja | Hermes 2 Pro |
+  | nvidia-Eagle2-9B.jinja | Hermes 2 Pro |
+  | nvidia-Llama-3.1-Nemotron-70B-Instruct-HF.jinja | Llama 3.x |
+  | onnx-community-DeepSeek-R1-Distill-Qwen-1.5B-ONNX.jinja | DeepSeek R1 (extract reasoning) |
+  | open-thoughts-OpenThinker-7B.jinja | Hermes 2 Pro |
+  | openchat-openchat-3.5-0106.jinja | Generic |
+  | pankajmathur-orca_mini_v6_8b.jinja | Generic |
+  | princeton-nlp-Mistral-7B-Base-SFT-RDPO.jinja | Generic |
+  | princeton-nlp-Mistral-7B-Instruct-DPO.jinja | Generic |
+  | princeton-nlp-Mistral-7B-Instruct-RDPO.jinja | Generic |
+  | prithivMLmods-Bellatrix-Tiny-1.5B-R1.jinja | Hermes 2 Pro |
+  | prithivMLmods-Bellatrix-Tiny-1B-R1.jinja | Llama 3.x |
+  | prithivMLmods-Bellatrix-Tiny-1B-v3.jinja | Generic |
+  | prithivMLmods-Bellatrix-Tiny-3B-R1.jinja | Llama 3.x |
+  | prithivMLmods-Blaze-14B-xElite.jinja | Generic |
+  | prithivMLmods-Calcium-Opus-14B-Elite2-R1.jinja | Hermes 2 Pro |
+  | prithivMLmods-Calme-Ties-78B.jinja | Generic |
+  | prithivMLmods-Calme-Ties2-78B.jinja | Generic |
+  | prithivMLmods-Calme-Ties3-78B.jinja | Generic |
+  | prithivMLmods-ChemQwen2-vL.jinja | Generic |
+  | prithivMLmods-GWQ2b.jinja | Generic |
+  | prithivMLmods-LatexMind-2B-Codec.jinja | Generic |
+  | prithivMLmods-Llama-3.2-6B-AlgoCode.jinja | Llama 3.x |
+  | prithivMLmods-Megatron-Opus-14B-Exp.jinja | Hermes 2 Pro |
+  | prithivMLmods-Megatron-Opus-14B-Stock.jinja | Hermes 2 Pro |
+  | prithivMLmods-Megatron-Opus-7B-Exp.jinja | Hermes 2 Pro |
+  | prithivMLmods-Omni-Reasoner-Merged.jinja | Hermes 2 Pro |
+  | prithivMLmods-Omni-Reasoner4-Merged.jinja | Hermes 2 Pro |
+  | prithivMLmods-Primal-Opus-14B-Optimus-v1.jinja | Hermes 2 Pro |
+  | prithivMLmods-QwQ-Math-IO-500M.jinja | Hermes 2 Pro |
+  | prithivMLmods-Qwen-7B-Distill-Reasoner.jinja | DeepSeek R1 (extract reasoning) |
+  | prithivMLmods-Qwen2.5-1.5B-DeepSeek-R1-Instruct.jinja | Hermes 2 Pro |
+  | prithivMLmods-Qwen2.5-14B-DeepSeek-R1-1M.jinja | Hermes 2 Pro |
+  | prithivMLmods-Qwen2.5-32B-DeepSeek-R1-Instruct.jinja | Hermes 2 Pro |
+  | prithivMLmods-Qwen2.5-7B-DeepSeek-R1-1M.jinja | Hermes 2 Pro |
+  | prithivMLmods-Triangulum-v2-10B.jinja | Hermes 2 Pro |
+  | qingy2024-Falcon3-2x10B-MoE-Instruct.jinja | Hermes 2 Pro |
+  | rubenroy-Zurich-14B-GCv2-5m.jinja | Hermes 2 Pro |
+  | rubenroy-Zurich-7B-GCv2-5m.jinja | Hermes 2 Pro |
+  | silma-ai-SILMA-Kashif-2B-Instruct-v1.0.jinja | Generic |
+  | simplescaling-s1-32B.jinja | Hermes 2 Pro |
+  | sometimesanotion-Lamarck-14B-v0.7.jinja | Hermes 2 Pro |
+  | sonthenguyen-zephyr-sft-bnb-4bit-DPO-mtbr-180steps.jinja | Generic |
+  | sthenno-tempesthenno-icy-0130.jinja | Generic |
+  | sumink-qwft.jinja | Hermes 2 Pro |
+  | teknium-OpenHermes-2.5-Mistral-7B.jinja | Generic |
+  | thirdeyeai-elevate360m.jinja | Generic |
+  | tiiuae-Falcon3-10B-Instruct.jinja | Hermes 2 Pro |
+  | unsloth-DeepSeek-R1-Distill-Llama-8B-unsloth-bnb-4bit.jinja | DeepSeek R1 (extract reasoning) |
+  | unsloth-DeepSeek-R1-Distill-Llama-8B.jinja | DeepSeek R1 (extract reasoning) |
+  | unsloth-DeepSeek-R1.jinja | DeepSeek R1 (extract reasoning) |
+  | unsloth-Mistral-Small-24B-Instruct-2501-unsloth-bnb-4bit.jinja | Generic |
+  | upstage-solar-pro-preview-instruct.jinja | Generic |
+  | whyhow-ai-PatientSeek.jinja | Generic |
+  | xwen-team-Xwen-72B-Chat.jinja | Hermes 2 Pro |
+  | xwen-team-Xwen-7B-Chat.jinja | Hermes 2 Pro |
 
   This table can be generated with:
 
   ```bash
   ./build/bin/test-chat ../minja/build/tests/*.jinja 2>/dev/null
+  ```
 
   </details>
 
@@ -1202,11 +1394,20 @@ curl http://localhost:8080/v1/chat/completions \
 
   ```shell
   # Native support:
+
   llama-server --jinja -fa -hf bartowski/Qwen2.5-7B-Instruct-GGUF:Q4_K_M
   llama-server --jinja -fa -hf bartowski/Mistral-Nemo-Instruct-2407-GGUF:Q6_K_L
   llama-server --jinja -fa -hf bartowski/functionary-small-v3.2-GGUF:Q4_K_M
   llama-server --jinja -fa -hf bartowski/Llama-3.3-70B-Instruct-GGUF:Q4_K_M
 
+  # Native support for DeepSeek R1 works best w/ our own template (official template buggy)
+
+  llama-server --jinja -fa -hf bartowski/DeepSeek-R1-Distill-Qwen-7B-GGUF:Q6_K_L \
+    --chat-template-file models/templates/llama-cpp-deepseek-r1.jinja
+
+  llama-server --jinja -fa -hf bartowski/DeepSeek-R1-Distill-Qwen-32B-GGUF:Q4_K_M \
+    --chat-template-file models/templates/llama-cpp-deepseek-r1.jinja
+
   # Native support requires the right template for these GGUFs:
 
   llama-server --jinja -fa -hf bartowski/Hermes-2-Pro-Llama-3-8B-GGUF:Q4_K_M \
diff --git a/examples/server/server.cpp b/examples/server/server.cpp
index 0718806c8..9c5729dbc 100644
--- a/examples/server/server.cpp
+++ b/examples/server/server.cpp
@@ -173,6 +173,7 @@ struct slot_params {
             {"grammar_trigger_words",     grammar_trigger_words},
             {"grammar_trigger_tokens",    sampling.grammar_trigger_tokens},
             {"preserved_tokens",          sampling.preserved_tokens},
+            {"chat_format",               common_chat_format_name(oaicompat_chat_format)},
             {"samplers",                  samplers},
             {"speculative.n_max",         speculative.n_max},
             {"speculative.n_min",         speculative.n_min},
@@ -724,9 +725,19 @@ struct server_task_result_cmpl_final : server_task_result {
             msg.content = content;
         }
 
-        json tool_calls;
+        json message {
+            {"role", "assistant"},
+        };
+        if (!msg.reasoning_content.empty()) {
+            message["reasoning_content"] = msg.reasoning_content;
+        }
+        if (msg.content == "" && !msg.tool_calls.empty()) {
+            message["content"] = json();
+        } else {
+            message["content"] = msg.content;
+        }
         if (!msg.tool_calls.empty()) {
-            tool_calls = json::array();
+            auto tool_calls = json::array();
             for (const auto & tc : msg.tool_calls) {
                 tool_calls.push_back({
                     {"type", "function"},
@@ -737,15 +748,7 @@ struct server_task_result_cmpl_final : server_task_result {
                     {"id", tc.id},
                 });
             }
-        }
-
-        json message {
-            {"content", msg.content},
-            {"tool_calls", tool_calls},
-            {"role", "assistant"},
-        };
-        if (!msg.tool_plan.empty()) {
-            message["tool_plan"] = msg.tool_plan;
+            message["tool_calls"] = tool_calls;
         }
 
         json choice {
@@ -4056,7 +4059,7 @@ int main(int argc, char ** argv) {
         }
 
         auto body = json::parse(req.body);
-        json data = oaicompat_completion_params_parse(body, params.use_jinja, ctx_server.chat_templates);
+        json data = oaicompat_completion_params_parse(body, params.use_jinja, params.reasoning_format, ctx_server.chat_templates);
 
         return handle_completions_impl(
             SERVER_TASK_TYPE_COMPLETION,
@@ -4069,7 +4072,7 @@ int main(int argc, char ** argv) {
     // same with handle_chat_completions, but without inference part
     const auto handle_apply_template = [&ctx_server, &params, &res_ok](const httplib::Request & req, httplib::Response & res) {
         auto body = json::parse(req.body);
-        json data = oaicompat_completion_params_parse(body, params.use_jinja, ctx_server.chat_templates);
+        json data = oaicompat_completion_params_parse(body, params.use_jinja, params.reasoning_format, ctx_server.chat_templates);
         res_ok(res, {{ "prompt", std::move(data.at("prompt")) }});
     };
 
diff --git a/examples/server/tests/unit/test_tool_call.py b/examples/server/tests/unit/test_tool_call.py
index 4a551404f..ba3367b4f 100644
--- a/examples/server/tests/unit/test_tool_call.py
+++ b/examples/server/tests/unit/test_tool_call.py
@@ -92,6 +92,7 @@ def do_test_completion_with_required_tool_tiny(template_name: str, tool: dict, a
     tool_calls = choice["message"].get("tool_calls")
     assert tool_calls and len(tool_calls) == 1, f'Expected 1 tool call in {choice["message"]}'
     tool_call = tool_calls[0]
+    assert choice["message"].get("content") is None, f'Expected no content in {choice["message"]}'
     expected_function_name = "python" if tool["type"] == "code_interpreter" else tool["function"]["name"]
     assert expected_function_name == tool_call["function"]["name"]
     actual_arguments = tool_call["function"]["arguments"]
@@ -155,11 +156,11 @@ def test_completion_with_required_tool_tiny_slow(template_name: str, tool: dict,
 
     (TEST_TOOL,    "success",  "bartowski/Hermes-2-Pro-Llama-3-8B-GGUF:Q4_K_M", ("NousResearch/Hermes-2-Pro-Llama-3-8B", "tool_use")),
     (PYTHON_TOOL,  "code",     "bartowski/Hermes-2-Pro-Llama-3-8B-GGUF:Q4_K_M", ("NousResearch/Hermes-2-Pro-Llama-3-8B", "tool_use")),
-    (PYTHON_TOOL,  "code",     "bartowski/Hermes-2-Pro-Llama-3-8B-GGUF:Q4_K_M", "chatml"),
+    # (PYTHON_TOOL,  "code",     "bartowski/Hermes-2-Pro-Llama-3-8B-GGUF:Q4_K_M", "chatml"),
 
     (TEST_TOOL,    "success",  "bartowski/Hermes-3-Llama-3.1-8B-GGUF:Q4_K_M",   ("NousResearch/Hermes-3-Llama-3.1-8B", "tool_use")),
     (PYTHON_TOOL,  "code",     "bartowski/Hermes-3-Llama-3.1-8B-GGUF:Q4_K_M",   ("NousResearch/Hermes-3-Llama-3.1-8B", "tool_use")),
-    (PYTHON_TOOL,  "code",     "bartowski/Hermes-3-Llama-3.1-8B-GGUF:Q4_K_M",   "chatml"),
+    # (PYTHON_TOOL,  "code",     "bartowski/Hermes-3-Llama-3.1-8B-GGUF:Q4_K_M",   "chatml"),
 
     (TEST_TOOL,    "success",  "bartowski/Mistral-Nemo-Instruct-2407-GGUF:Q4_K_M", None),
     (PYTHON_TOOL,  "code",     "bartowski/Mistral-Nemo-Instruct-2407-GGUF:Q4_K_M", None),
@@ -175,7 +176,7 @@ def test_completion_with_required_tool_tiny_slow(template_name: str, tool: dict,
 
     (TEST_TOOL,    "success",  "bartowski/Llama-3.2-1B-Instruct-GGUF:Q4_K_M",      ("meta-llama/Llama-3.2-3B-Instruct", None)),
     (PYTHON_TOOL,  "code",     "bartowski/Llama-3.2-1B-Instruct-GGUF:Q4_K_M",      ("meta-llama/Llama-3.2-3B-Instruct", None)),
-    (PYTHON_TOOL,  "code",     "bartowski/Llama-3.2-1B-Instruct-GGUF:Q4_K_M",      "chatml"),
+    # (PYTHON_TOOL,  "code",     "bartowski/Llama-3.2-1B-Instruct-GGUF:Q4_K_M",      "chatml"),
     # TODO: fix these
     # (TEST_TOOL,    "success",  "bartowski/DeepSeek-R1-Distill-Qwen-7B-GGUF:Q4_K_M", None),
     # (PYTHON_TOOL,  "code",     "bartowski/DeepSeek-R1-Distill-Qwen-7B-GGUF:Q4_K_M", None),
@@ -214,6 +215,7 @@ def test_completion_with_required_tool_real_model(tool: dict, argument_key: str
     tool_calls = choice["message"].get("tool_calls")
     assert tool_calls and len(tool_calls) == 1, f'Expected 1 tool call in {choice["message"]}'
     tool_call = tool_calls[0]
+    assert choice["message"].get("content") is None, f'Expected no content in {choice["message"]}'
     expected_function_name = "python" if tool["type"] == "code_interpreter" else tool["function"]["name"]
     assert expected_function_name == tool_call["function"]["name"]
     actual_arguments = tool_call["function"]["arguments"]
@@ -273,7 +275,6 @@ def test_completion_without_tool_call_slow(template_name: str, n_predict: int, t
 
 @pytest.mark.slow
 @pytest.mark.parametrize("hf_repo,template_override", [
-    ("bartowski/c4ai-command-r7b-12-2024-GGUF:Q4_K_M",   ("CohereForAI/c4ai-command-r7b-12-2024", "tool_use")),
     ("bartowski/Meta-Llama-3.1-8B-Instruct-GGUF:Q4_K_M", None),
     ("bartowski/Meta-Llama-3.1-8B-Instruct-GGUF:Q4_K_M", "chatml"),
 
@@ -298,13 +299,16 @@ def test_completion_without_tool_call_slow(template_name: str, n_predict: int, t
     ("bartowski/Llama-3.2-3B-Instruct-GGUF:Q4_K_M",      ("meta-llama/Llama-3.2-3B-Instruct", None)),
     ("bartowski/Llama-3.2-3B-Instruct-GGUF:Q4_K_M",      "chatml"),
 
+    ("bartowski/c4ai-command-r7b-12-2024-GGUF:Q6_K_L",   ("CohereForAI/c4ai-command-r7b-12-2024", "tool_use")),
+
+    ("bartowski/DeepSeek-R1-Distill-Qwen-7B-GGUF:Q4_K_M", None),
+
     # Note: gemma-2-2b-it knows itself as "model", not "assistant", so we don't test the ill-suited chatml on it.
     ("bartowski/gemma-2-2b-it-GGUF:Q4_K_M",              None),
 
     # ("bartowski/Llama-3.2-1B-Instruct-GGUF:Q4_K_M", ("meta-llama/Llama-3.2-3B-Instruct", None)),
-    # ("bartowski/DeepSeek-R1-Distill-Qwen-7B-GGUF:Q4_K_M", None),
 ])
-def test_weather(hf_repo: str, template_override: Tuple[str, str | None] | None):
+def test_weather(hf_repo: str, template_override: str | Tuple[str, str | None] | None):
     global server
     n_predict = 512
     server.n_slots = 1
@@ -323,6 +327,7 @@ def test_weather(hf_repo: str, template_override: Tuple[str, str | None] | None)
     res = server.make_request("POST", "/chat/completions", data={
         "max_tokens": n_predict,
         "messages": [
+            {"role": "system", "content": "You are a chatbot that uses tools/functions. Dont overthink things."},
             {"role": "user", "content": "What is the weather in Istanbul?"},
         ],
         "tools": [WEATHER_TOOL],
@@ -332,6 +337,7 @@ def test_weather(hf_repo: str, template_override: Tuple[str, str | None] | None)
     tool_calls = choice["message"].get("tool_calls")
     assert tool_calls and len(tool_calls) == 1, f'Expected 1 tool call in {choice["message"]}'
     tool_call = tool_calls[0]
+    assert choice["message"].get("content") is None, f'Expected no content in {choice["message"]}'
     assert tool_call["function"]["name"] == WEATHER_TOOL["function"]["name"]
     actual_arguments = json.loads(tool_call["function"]["arguments"])
     assert 'location' in actual_arguments, f"location not found in {json.dumps(actual_arguments)}"
@@ -340,22 +346,166 @@ def test_weather(hf_repo: str, template_override: Tuple[str, str | None] | None)
     assert re.match('^Istanbul(, (TR|Turkey|Türkiye))?$', location), f'Expected Istanbul for location, got {location}'
 
 
+@pytest.mark.slow
+@pytest.mark.parametrize("result_override,n_predict,hf_repo,template_override", [
+    (None,                                           128,  "bartowski/Phi-3.5-mini-instruct-GGUF:Q4_K_M",       "chatml"),
+    (None,                                           128,  "bartowski/Qwen2.5-7B-Instruct-GGUF:Q4_K_M",         None),
+    (None,                                           128,  "bartowski/Qwen2.5-7B-Instruct-GGUF:Q4_K_M",         "chatml"),
+    (None,                                           128,  "bartowski/Hermes-2-Pro-Llama-3-8B-GGUF:Q4_K_M",     ("NousResearch/Hermes-2-Pro-Llama-3-8B", "tool_use")),
+    (None,                                           128,  "bartowski/Hermes-3-Llama-3.1-8B-GGUF:Q4_K_M",       ("NousResearch/Hermes-3-Llama-3.1-8B", "tool_use")),
+    (None,                                           128,  "bartowski/functionary-small-v3.2-GGUF:Q8_0",        ("meetkai/functionary-medium-v3.2", None)),
+    (None,                                           128,  "bartowski/Meta-Llama-3.1-8B-Instruct-GGUF:Q4_K_M",  None),
+    (None,                                           128,  "bartowski/Mistral-Nemo-Instruct-2407-GGUF:Q4_K_M",  None),
+    ("^> 0.56$",                                     128,  "bartowski/Mistral-Nemo-Instruct-2407-GGUF:Q4_K_M",  "chatml"),
+    (None,                                           128,  "bartowski/Phi-3.5-mini-instruct-GGUF:Q4_K_M",       None),
+
+    # TODO: fix these (wrong results, either didn't respect decimal instruction or got wrong value)
+    ("^The y-coordinate [\\s\\S]*?\\*\\*0.5\\*\\*",  8192, "bartowski/DeepSeek-R1-Distill-Qwen-7B-GGUF:Q4_K_M", None),
+    ("[\\s\\S]*?\\*\\*0\\.5\\*\\*",                  8192, "bartowski/DeepSeek-R1-Distill-Qwen-7B-GGUF:Q4_K_M", ("llama-cpp-deepseek-r1", None)),
+])
+def test_calc_result(result_override: str | None, n_predict: int, hf_repo: str, template_override: str | Tuple[str, str | None] | None):
+    global server
+    # n_predict = 512
+    server.n_slots = 1
+    server.jinja = True
+    server.n_ctx = 8192 * 2
+    server.n_predict = n_predict
+    server.model_hf_repo = hf_repo
+    server.model_hf_file = None
+    if isinstance(template_override, tuple):
+        (template_hf_repo, template_variant) = template_override
+        server.chat_template_file = f"../../../models/templates/{template_hf_repo.replace('/', '-') + ('-' + template_variant if template_variant else '')}.jinja"
+        assert os.path.exists(server.chat_template_file), f"Template file {server.chat_template_file} does not exist. Run `python scripts/get_chat_template.py {template_hf_repo} {template_variant} > {server.chat_template_file}` to download the template."
+    elif isinstance(template_override, str):
+        server.chat_template = template_override
+    server.start(timeout_seconds=TIMEOUT_SERVER_START)
+    res = server.make_request("POST", "/chat/completions", data={
+        "max_tokens": n_predict,
+        "messages": [
+            {"role": "system", "content": "You are a chatbot that uses tools/functions. Dont overthink things, and provide very concise answers. Do not explain your reasoning to the user. Provide any numerical values back to the user with at most two decimals."},
+            {"role": "user", "content": "What's the y coordinate of a point on the unit sphere at angle 30 degrees?"},
+            {
+                "role": "assistant",
+                "content": None,
+                "tool_calls": [
+                    {
+                        "id": "call_6789",
+                        "type": "function",
+                        "function": {
+                            "name": "calculate",
+                            "arguments": "{\"expression\":\"sin(30 * pi / 180)\"}"
+                        }
+                    }
+                ]
+            },
+            {
+                "role": "tool",
+                "name": "calculate",
+                "content": 0.55644242476,
+                "tool_call_id": "call_6789"
+            }
+        ],
+        "tools": [
+            {
+                "type":"function",
+                "function":{
+                    "name":"calculate",
+                    "description":"A calculator function that computes values of arithmetic expressions in the Python syntax",
+                    "parameters":{
+                        "type":"object",
+                        "properties":{
+                            "expression":{
+                            "type":"string",
+                            "description":"An arithmetic expression to compute the value of (Python syntad, assuming all floats)"
+                            }
+                        },
+                        "required":["expression"]
+                    }
+                }
+            }
+        ]
+    }, timeout=TIMEOUT_HTTP_REQUEST)
+    assert res.status_code == 200, f"Expected status code 200, got {res.status_code}"
+    choice = res.body["choices"][0]
+    tool_calls = choice["message"].get("tool_calls")
+    assert tool_calls is None, f'Expected no tool call in {choice["message"]}'
+    content = choice["message"].get("content")
+    assert content is not None, f'Expected content in {choice["message"]}'
+    if result_override is not None:
+        assert re.match(result_override, content), f'Expected {result_override}, got {content}'
+    else:
+        assert re.match('^[\\s\\S]*?The (y[ -])?coordinate [\\s\\S]*?is (approximately )?0\\.56\\b|^0\\.56$', content), \
+            f'Expected something like "The y coordinate is 0.56.", got {content}'
+
+
+@pytest.mark.slow
+@pytest.mark.parametrize("n_predict,reasoning_format,expect_content,expect_reasoning_content,hf_repo,template_override", [
+    (128, 'deepseek',  "^The sum of 102 and 7 is 109.*",                        None,                                          "bartowski/Phi-3.5-mini-instruct-GGUF:Q4_K_M",       None),
+    (128,  None,        "^The sum of 102 and 7 is 109.*",                       None,                                          "bartowski/Phi-3.5-mini-instruct-GGUF:Q4_K_M",       None),
+
+    (1024, 'deepseek',  "To find the sum of.*",                                 "I need to calculate the sum of 102 and 7.*",  "bartowski/DeepSeek-R1-Distill-Qwen-7B-GGUF:Q4_K_M", None),
+    (1024, 'none',      "<think>\n?I need[\\s\\S]*?</think>\n?To find.*",       None,                                          "bartowski/DeepSeek-R1-Distill-Qwen-7B-GGUF:Q4_K_M", None),
+
+    (1024, 'deepseek',  "To find the sum of.*",                                 "First, I [\\s\\S]*",                          "bartowski/DeepSeek-R1-Distill-Qwen-7B-GGUF:Q4_K_M", ("llama-cpp-deepseek-r1", None)),
+])
+def test_thoughts(n_predict: int, reasoning_format: Literal['deepseek', 'none'] | None, expect_content: str | None, expect_reasoning_content: str | None, hf_repo: str, template_override: str | Tuple[str, str | None] | None):
+    global server
+    server.n_slots = 1
+    server.reasoning_format = reasoning_format
+    server.jinja = True
+    server.n_ctx = 8192 * 2
+    server.n_predict = n_predict
+    server.model_hf_repo = hf_repo
+    server.model_hf_file = None
+    if isinstance(template_override, tuple):
+        (template_hf_repo, template_variant) = template_override
+        server.chat_template_file = f"../../../models/templates/{template_hf_repo.replace('/', '-') + ('-' + template_variant if template_variant else '')}.jinja"
+        assert os.path.exists(server.chat_template_file), f"Template file {server.chat_template_file} does not exist. Run `python scripts/get_chat_template.py {template_hf_repo} {template_variant} > {server.chat_template_file}` to download the template."
+    elif isinstance(template_override, str):
+        server.chat_template = template_override
+    server.start(timeout_seconds=TIMEOUT_SERVER_START)
+    res = server.make_request("POST", "/chat/completions", data={
+        "max_tokens": n_predict,
+        "messages": [
+            {"role": "user", "content": "What's the sum of 102 and 7?"},
+        ]
+    }, timeout=TIMEOUT_HTTP_REQUEST)
+    assert res.status_code == 200, f"Expected status code 200, got {res.status_code}"
+    choice = res.body["choices"][0]
+    assert choice["message"].get("tool_calls") is None, f'Expected no tool call in {choice["message"]}'
+
+    content = choice["message"].get("content")
+    if expect_content is None:
+        assert content is None, f'Expected no content in {choice["message"]}'
+    else:
+        assert re.match(expect_content, content), f'Expected {expect_content}, got {content}'
+
+    reasoning_content = choice["message"].get("reasoning_content")
+    if expect_reasoning_content is None:
+        assert reasoning_content is None, f'Expected no reasoning content in {choice["message"]}'
+    else:
+        assert re.match(expect_reasoning_content, reasoning_content), f'Expected {expect_reasoning_content}, got {reasoning_content}'
+
+
 @pytest.mark.slow
 @pytest.mark.parametrize("expected_arguments_override,hf_repo,template_override", [
+    (None,                 "bartowski/DeepSeek-R1-Distill-Qwen-7B-GGUF:Q4_K_M", None),
+    # (None,                 "bartowski/DeepSeek-R1-Distill-Qwen-7B-GGUF:Q4_K_M", "chatml"),
+
     (None,                 "bartowski/Phi-3.5-mini-instruct-GGUF:Q4_K_M",      None),
     (None,                 "bartowski/Phi-3.5-mini-instruct-GGUF:Q4_K_M",      "chatml"),
 
     (None,                 "bartowski/functionary-small-v3.2-GGUF:Q8_0",       ("meetkai-functionary-medium-v3.2", None)),
     (None,                 "bartowski/functionary-small-v3.2-GGUF:Q8_0",       "chatml"),
 
-    (None,                 "bartowski/Meta-Llama-3.1-8B-Instruct-GGUF:Q4_K_M", None),
-    ('{"code":"print("}',  "bartowski/Meta-Llama-3.1-8B-Instruct-GGUF:Q4_K_M", "chatml"),
+    ('{"code":"print("}',  "bartowski/Meta-Llama-3.1-8B-Instruct-GGUF:Q4_K_M", None),
+    (None,                 "bartowski/Meta-Llama-3.1-8B-Instruct-GGUF:Q4_K_M", "chatml"),
 
-    ('{"code":"print("}',  "bartowski/Llama-3.2-1B-Instruct-GGUF:Q4_K_M",      ("meta-llama-Llama-3.2-3B-Instruct", None)),
+    (None,                 "bartowski/Llama-3.2-1B-Instruct-GGUF:Q4_K_M",      ("meta-llama-Llama-3.2-3B-Instruct", None)),
     (None,                 "bartowski/Llama-3.2-1B-Instruct-GGUF:Q4_K_M",      "chatml"),
 
     ('{"code":"print("}',  "bartowski/Llama-3.2-3B-Instruct-GGUF:Q4_K_M",      ("meta-llama-Llama-3.2-3B-Instruct", None)),
-    ('{"code":"print("}',  "bartowski/Llama-3.2-3B-Instruct-GGUF:Q4_K_M",      "chatml"),
+    (None,                 "bartowski/Llama-3.2-3B-Instruct-GGUF:Q4_K_M",      "chatml"),
 
     (None,                 "bartowski/Qwen2.5-7B-Instruct-GGUF:Q4_K_M",        None),
     (None,                 "bartowski/Qwen2.5-7B-Instruct-GGUF:Q4_K_M",        "chatml"),
@@ -371,15 +521,13 @@ def test_weather(hf_repo: str, template_override: Tuple[str, str | None] | None)
 
     # Note: gemma-2-2b-it knows itself as "model", not "assistant", so we don't test the ill-suited chatml on it.
     (None,                 "bartowski/gemma-2-2b-it-GGUF:Q4_K_M",              None),
-
-    # (None,                 "bartowski/DeepSeek-R1-Distill-Qwen-7B-GGUF:Q4_K_M", None),
 ])
-def test_hello_world_tool_call(expected_arguments_override: str | None, hf_repo: str, template_override: str | Tuple[str, str | None] | None):
+def test_hello_world(expected_arguments_override: str | None, hf_repo: str, template_override: str | Tuple[str, str | None] | None):
     global server
     server.n_slots = 1
     server.jinja = True
     server.n_ctx = 8192
-    server.n_predict = 128
+    server.n_predict = 512 # High because of DeepSeek R1
     server.model_hf_repo = hf_repo
     server.model_hf_file = None
     if isinstance(template_override, tuple):
@@ -406,6 +554,7 @@ def test_hello_world_tool_call(expected_arguments_override: str | None, hf_repo:
     tool_calls = choice["message"].get("tool_calls")
     assert tool_calls and len(tool_calls) == 1, f'Expected 1 tool call in {choice["message"]}'
     tool_call = tool_calls[0]
+    assert choice["message"].get("content") is None, f'Expected no content in {choice["message"]}'
     assert tool_call["function"]["name"] == PYTHON_TOOL["function"]["name"]
     actual_arguments = tool_call["function"]["arguments"]
     if expected_arguments_override is not None:
diff --git a/examples/server/tests/utils.py b/examples/server/tests/utils.py
index ce0680662..a82504235 100644
--- a/examples/server/tests/utils.py
+++ b/examples/server/tests/utils.py
@@ -78,6 +78,7 @@ class ServerProcess:
     draft_max: int | None = None
     no_webui: bool | None = None
     jinja: bool | None = None
+    reasoning_format: Literal['deepseek', 'none'] | None = None
     chat_template: str | None = None
     chat_template_file: str | None = None
 
@@ -172,6 +173,8 @@ class ServerProcess:
             server_args.append("--no-webui")
         if self.jinja:
             server_args.append("--jinja")
+        if self.reasoning_format is not None:
+            server_args.extend(("--reasoning-format", self.reasoning_format))
         if self.chat_template:
             server_args.extend(["--chat-template", self.chat_template])
         if self.chat_template_file:
diff --git a/examples/server/utils.hpp b/examples/server/utils.hpp
index 5f97df5fd..86de0e6d7 100644
--- a/examples/server/utils.hpp
+++ b/examples/server/utils.hpp
@@ -578,6 +578,7 @@ static json oaicompat_completion_params_parse(const json & body) {
 static json oaicompat_completion_params_parse(
     const json & body, /* openai api json semantics */
     bool use_jinja,
+    common_reasoning_format reasoning_format,
     const common_chat_templates & chat_templates)
 {
     json llama_params;
@@ -633,9 +634,10 @@ static json oaicompat_completion_params_parse(
             throw std::runtime_error("Cannot use custom grammar constraints with tools.");
         }
         common_chat_inputs inputs;
-        inputs.messages = body.at("messages");
-        inputs.tools = tools;
-        inputs.tool_choice = tool_choice;
+        inputs.extract_reasoning   = reasoning_format != COMMON_REASONING_FORMAT_NONE;
+        inputs.messages            = body.at("messages");
+        inputs.tools               = tools;
+        inputs.tool_choice         = tool_choice;
         inputs.parallel_tool_calls = json_value(body, "parallel_tool_calls", false);
         if (inputs.parallel_tool_calls && !tmpl.original_caps().supports_parallel_tool_calls) {
             LOG_DBG("Disabling parallel_tool_calls because the template does not support it\n");
diff --git a/models/templates/README.md b/models/templates/README.md
new file mode 100644
index 000000000..72c30d1e1
--- /dev/null
+++ b/models/templates/README.md
@@ -0,0 +1,22 @@
+These templates can be updated with the following commands:
+
+```bash
+./scripts/get_chat_template.py CohereForAI/c4ai-command-r-plus tool_use      > models/templates/CohereForAI-c4ai-command-r-plus-tool_use.jinja
+./scripts/get_chat_template.py CohereForAI/c4ai-command-r7b-12-2024 default  > models/templates/CohereForAI-c4ai-command-r7b-12-2024-default.jinja
+./scripts/get_chat_template.py CohereForAI/c4ai-command-r7b-12-2024 rag      > models/templates/CohereForAI-c4ai-command-r7b-12-2024-rag.jinja
+./scripts/get_chat_template.py CohereForAI/c4ai-command-r7b-12-2024 tool_use > models/templates/CohereForAI-c4ai-command-r7b-12-2024-tool_use.jinja
+./scripts/get_chat_template.py deepseek-ai/DeepSeek-R1-Distill-Llama-8B      > models/templates/deepseek-ai-DeepSeek-R1-Distill-Llama-8B.jinja
+./scripts/get_chat_template.py deepseek-ai/DeepSeek-R1-Distill-Qwen-32B      > models/templates/deepseek-ai-DeepSeek-R1-Distill-Qwen-32B.jinja
+./scripts/get_chat_template.py fireworks-ai/llama-3-firefunction-v2          > models/templates/fireworks-ai-llama-3-firefunction-v2.jinja
+./scripts/get_chat_template.py google/gemma-2-2b-it                          > models/templates/google-gemma-2-2b-it.jinja
+./scripts/get_chat_template.py meetkai/functionary-medium-v3.                > models/templates/meetkai-functionary-medium-v3.jinja
+./scripts/get_chat_template.py meetkai/functionary-medium-v3.2               > models/templates/meetkai-functionary-medium-v3.2.jinja
+./scripts/get_chat_template.py meta-llama/Llama-3.1-8B-Instruct              > models/templates/meta-llama-Llama-3.1-8B-Instruct.jinja
+./scripts/get_chat_template.py meta-llama/Llama-3.2-3B-Instruct              > models/templates/meta-llama-Llama-3.2-3B-Instruct.jinja
+./scripts/get_chat_template.py meta-llama/Llama-3.3-70B-Instruct             > models/templates/meta-llama-Llama-3.3-70B-Instruct.jinja
+./scripts/get_chat_template.py microsoft/Phi-3.5-mini-instruct               > models/templates/microsoft-Phi-3.5-mini-instruct.jinja
+./scripts/get_chat_template.py mistralai/Mistral-Nemo-Instruct-2407          > models/templates/mistralai-Mistral-Nemo-Instruct-2407.jinja
+./scripts/get_chat_template.py NousResearch/Hermes-2-Pro-Llama-3-8B tool_use > models/templates/NousResearch-Hermes-2-Pro-Llama-3-8B-tool_use.jinja
+./scripts/get_chat_template.py NousResearch/Hermes-3-Llama-3.1-8B tool_use   > models/templates/NousResearch-Hermes-3-Llama-3.1-8B-tool_use.jinja
+./scripts/get_chat_template.py Qwen/Qwen2.5-7B-Instruct                      > models/templates/Qwen-Qwen2.5-7B-Instruct.jinja
+```
\ No newline at end of file
diff --git a/models/templates/deepseek-ai-DeepSeek-R1-Distill-Llama-8B.jinja b/models/templates/deepseek-ai-DeepSeek-R1-Distill-Llama-8B.jinja
index 02a1c3bce..c2066bd73 100644
--- a/models/templates/deepseek-ai-DeepSeek-R1-Distill-Llama-8B.jinja
+++ b/models/templates/deepseek-ai-DeepSeek-R1-Distill-Llama-8B.jinja
@@ -1 +1 @@
-{% if not add_generation_prompt is defined %}{% set add_generation_prompt = false %}{% endif %}{% set ns = namespace(is_first=false, is_tool=false, is_output_first=true, system_prompt='') %}{%- for message in messages %}{%- if message['role'] == 'system' %}{% set ns.system_prompt = message['content'] %}{%- endif %}{%- endfor %}{{bos_token}}{{ns.system_prompt}}{%- for message in messages %}{%- if message['role'] == 'user' %}{%- set ns.is_tool = false -%}{{'<｜User｜>' + message['content']}}{%- endif %}{%- if message['role'] == 'assistant' and message['content'] is none %}{%- set ns.is_tool = false -%}{%- for tool in message['tool_calls']%}{%- if not ns.is_first %}{{'<｜Assistant｜><｜tool▁calls▁begin｜><｜tool▁call▁begin｜>' + tool['type'] + '<｜tool▁sep｜>' + tool['function']['name'] + '\n' + '```json' + '\n' + tool['function']['arguments'] + '\n' + '```' + '<｜tool▁call▁end｜>'}}{%- set ns.is_first = true -%}{%- else %}{{'\n' + '<｜tool▁call▁begin｜>' + tool['type'] + '<｜tool▁sep｜>' + tool['function']['name'] + '\n' + '```json' + '\n' + tool['function']['arguments'] + '\n' + '```' + '<｜tool▁call▁end｜>'}}{{'<｜tool▁calls▁end｜><｜end▁of▁sentence｜>'}}{%- endif %}{%- endfor %}{%- endif %}{%- if message['role'] == 'assistant' and message['content'] is not none %}{%- if ns.is_tool %}{{'<｜tool▁outputs▁end｜>' + message['content'] + '<｜end▁of▁sentence｜>'}}{%- set ns.is_tool = false -%}{%- else %}{% set content = message['content'] %}{% if '</think>' in content %}{% set content = content.split('</think>')[-1] %}{% endif %}{{'<｜Assistant｜>' + content + '<｜end▁of▁sentence｜>'}}{%- endif %}{%- endif %}{%- if message['role'] == 'tool' %}{%- set ns.is_tool = true -%}{%- if ns.is_output_first %}{{'<｜tool▁outputs▁begin｜><｜tool▁output▁begin｜>' + message['content'] + '<｜tool▁output▁end｜>'}}{%- set ns.is_output_first = false %}{%- else %}{{'\n<｜tool▁output▁begin｜>' + message['content'] + '<｜tool▁output▁end｜>'}}{%- endif %}{%- endif %}{%- endfor -%}{% if ns.is_tool %}{{'<｜tool▁outputs▁end｜>'}}{% endif %}{% if add_generation_prompt and not ns.is_tool %}{{'<｜Assistant｜>'}}{% endif %}
\ No newline at end of file
+{% if not add_generation_prompt is defined %}{% set add_generation_prompt = false %}{% endif %}{% set ns = namespace(is_first=false, is_tool=false, is_output_first=true, system_prompt='') %}{%- for message in messages %}{%- if message['role'] == 'system' %}{% set ns.system_prompt = message['content'] %}{%- endif %}{%- endfor %}{{bos_token}}{{ns.system_prompt}}{%- for message in messages %}{%- if message['role'] == 'user' %}{%- set ns.is_tool = false -%}{{'<｜User｜>' + message['content']}}{%- endif %}{%- if message['role'] == 'assistant' and message['content'] is none %}{%- set ns.is_tool = false -%}{%- for tool in message['tool_calls']%}{%- if not ns.is_first %}{{'<｜Assistant｜><｜tool▁calls▁begin｜><｜tool▁call▁begin｜>' + tool['type'] + '<｜tool▁sep｜>' + tool['function']['name'] + '\n' + '```json' + '\n' + tool['function']['arguments'] + '\n' + '```' + '<｜tool▁call▁end｜>'}}{%- set ns.is_first = true -%}{%- else %}{{'\n' + '<｜tool▁call▁begin｜>' + tool['type'] + '<｜tool▁sep｜>' + tool['function']['name'] + '\n' + '```json' + '\n' + tool['function']['arguments'] + '\n' + '```' + '<｜tool▁call▁end｜>'}}{{'<｜tool▁calls▁end｜><｜end▁of▁sentence｜>'}}{%- endif %}{%- endfor %}{%- endif %}{%- if message['role'] == 'assistant' and message['content'] is not none %}{%- if ns.is_tool %}{{'<｜tool▁outputs▁end｜>' + message['content'] + '<｜end▁of▁sentence｜>'}}{%- set ns.is_tool = false -%}{%- else %}{% set content = message['content'] %}{% if '</think>' in content %}{% set content = content.split('</think>')[-1] %}{% endif %}{{'<｜Assistant｜>' + content + '<｜end▁of▁sentence｜>'}}{%- endif %}{%- endif %}{%- if message['role'] == 'tool' %}{%- set ns.is_tool = true -%}{%- if ns.is_output_first %}{{'<｜tool▁outputs▁begin｜><｜tool▁output▁begin｜>' + message['content'] + '<｜tool▁output▁end｜>'}}{%- set ns.is_output_first = false %}{%- else %}{{'\n<｜tool▁output▁begin｜>' + message['content'] + '<｜tool▁output▁end｜>'}}{%- endif %}{%- endif %}{%- endfor -%}{% if ns.is_tool %}{{'<｜tool▁outputs▁end｜>'}}{% endif %}{% if add_generation_prompt and not ns.is_tool %}{{'<｜Assistant｜><think>\n'}}{% endif %}
\ No newline at end of file
diff --git a/models/templates/deepseek-ai-DeepSeek-R1-Distill-Qwen-32B.jinja b/models/templates/deepseek-ai-DeepSeek-R1-Distill-Qwen-32B.jinja
index 2ebfe7c1e..c2066bd73 100644
--- a/models/templates/deepseek-ai-DeepSeek-R1-Distill-Qwen-32B.jinja
+++ b/models/templates/deepseek-ai-DeepSeek-R1-Distill-Qwen-32B.jinja
@@ -1,56 +1 @@
-{% if not add_generation_prompt is defined %}
-{% set add_generation_prompt = false %}
-{% endif %}
-{% set ns = namespace(is_first=false, is_tool=false, is_output_first=true, system_prompt='') %}
-{%- for message in messages %}
-{%- if message['role'] == 'system' %}
-{% set ns.system_prompt = message['content'] %}
-{%- endif %}
-{%- endfor %}
-{{bos_token}}
-{{ns.system_prompt}}
-{%- for message in messages %}
-{%- if message['role'] == 'user' %}
-{%- set ns.is_tool = false -%}
-{{'<｜User｜>' + message['content']}}
-{%- endif %}
-{%- if message['role'] == 'assistant' and message['content'] is none %}
-{%- set ns.is_tool = false -%}
-{%- for tool in message['tool_calls']%}
-{%- if not ns.is_first %}
-{{'<｜Assistant｜><｜tool▁calls▁begin｜><｜tool▁call▁begin｜>' + tool['type'] + '<｜tool▁sep｜>' + tool['function']['name'] + '\n' + '```json' + '\n' + tool['function']['arguments'] + '\n' + '```' + '<｜tool▁call▁end｜>'}}
-{%- set ns.is_first = true -%}
-{%- else %}
-{{'\n' + '<｜tool▁call▁begin｜>' + tool['type'] + '<｜tool▁sep｜>' + tool['function']['name'] + '\n' + '```json' + '\n' + tool['function']['arguments'] + '\n' + '```' + '<｜tool▁call▁end｜>'}}
-{{'<｜tool▁calls▁end｜><｜end▁of▁sentence｜>'}}
-{%- endif %}
-{%- endfor %}
-{%- endif %}
-{%- if message['role'] == 'assistant' and message['content'] is not none %}
-{%- if ns.is_tool %}
-{{'<｜tool▁outputs▁end｜>' + message['content'] + '<｜end▁of▁sentence｜>'}}
-{%- set ns.is_tool = false -%}
-{%- else %}
-{% set content = message['content'] %}
-{% if '</think>' in content %}
-{% set content = content.split('</think>')[-1] %}
-{% endif %}
-{{'<｜Assistant｜>' + content + '<｜end▁of▁sentence｜>'}}
-{%- endif %}
-{%- endif %}
-{%- if message['role'] == 'tool' %}
-{%- set ns.is_tool = true -%}
-{%- if ns.is_output_first %}
-{{'<｜tool▁outputs▁begin｜><｜tool▁output▁begin｜>' + message['content'] + '<｜tool▁output▁end｜>'}}
-{%- set ns.is_output_first = false %}
-{%- else %}
-{{'\n<｜tool▁output▁begin｜>' + message['content'] + '<｜tool▁output▁end｜>'}}
-{%- endif %}
-{%- endif %}
-{%- endfor -%}
-{% if ns.is_tool %}
-{{'<｜tool▁outputs▁end｜>'}}
-{% endif %}
-{% if add_generation_prompt and not ns.is_tool %}
-{{'<｜Assistant｜>'}}
-{% endif %}
\ No newline at end of file
+{% if not add_generation_prompt is defined %}{% set add_generation_prompt = false %}{% endif %}{% set ns = namespace(is_first=false, is_tool=false, is_output_first=true, system_prompt='') %}{%- for message in messages %}{%- if message['role'] == 'system' %}{% set ns.system_prompt = message['content'] %}{%- endif %}{%- endfor %}{{bos_token}}{{ns.system_prompt}}{%- for message in messages %}{%- if message['role'] == 'user' %}{%- set ns.is_tool = false -%}{{'<｜User｜>' + message['content']}}{%- endif %}{%- if message['role'] == 'assistant' and message['content'] is none %}{%- set ns.is_tool = false -%}{%- for tool in message['tool_calls']%}{%- if not ns.is_first %}{{'<｜Assistant｜><｜tool▁calls▁begin｜><｜tool▁call▁begin｜>' + tool['type'] + '<｜tool▁sep｜>' + tool['function']['name'] + '\n' + '```json' + '\n' + tool['function']['arguments'] + '\n' + '```' + '<｜tool▁call▁end｜>'}}{%- set ns.is_first = true -%}{%- else %}{{'\n' + '<｜tool▁call▁begin｜>' + tool['type'] + '<｜tool▁sep｜>' + tool['function']['name'] + '\n' + '```json' + '\n' + tool['function']['arguments'] + '\n' + '```' + '<｜tool▁call▁end｜>'}}{{'<｜tool▁calls▁end｜><｜end▁of▁sentence｜>'}}{%- endif %}{%- endfor %}{%- endif %}{%- if message['role'] == 'assistant' and message['content'] is not none %}{%- if ns.is_tool %}{{'<｜tool▁outputs▁end｜>' + message['content'] + '<｜end▁of▁sentence｜>'}}{%- set ns.is_tool = false -%}{%- else %}{% set content = message['content'] %}{% if '</think>' in content %}{% set content = content.split('</think>')[-1] %}{% endif %}{{'<｜Assistant｜>' + content + '<｜end▁of▁sentence｜>'}}{%- endif %}{%- endif %}{%- if message['role'] == 'tool' %}{%- set ns.is_tool = true -%}{%- if ns.is_output_first %}{{'<｜tool▁outputs▁begin｜><｜tool▁output▁begin｜>' + message['content'] + '<｜tool▁output▁end｜>'}}{%- set ns.is_output_first = false %}{%- else %}{{'\n<｜tool▁output▁begin｜>' + message['content'] + '<｜tool▁output▁end｜>'}}{%- endif %}{%- endif %}{%- endfor -%}{% if ns.is_tool %}{{'<｜tool▁outputs▁end｜>'}}{% endif %}{% if add_generation_prompt and not ns.is_tool %}{{'<｜Assistant｜><think>\n'}}{% endif %}
\ No newline at end of file
diff --git a/models/templates/llama-cpp-deepseek-r1.jinja b/models/templates/llama-cpp-deepseek-r1.jinja
new file mode 100644
index 000000000..fcb1732eb
--- /dev/null
+++ b/models/templates/llama-cpp-deepseek-r1.jinja
@@ -0,0 +1,76 @@
+{%- if not add_generation_prompt is defined -%}
+    {%- set add_generation_prompt = false -%}
+{%- endif -%}
+{%- set ns = namespace(is_first=false, is_tool_outputs=false, is_output_first=true, system_prompt='') -%}
+{%- for message in messages -%}
+    {%- if message['role'] == 'system' -%}
+        {%- set ns.system_prompt = message['content'] -%}
+    {%- endif -%}
+{%- endfor -%}
+{{bos_token}}
+{%- if tools %}
+You can call any of the following function tools to satisfy the user's requests: {{tools | map(attribute='function') | tojson(indent=2)}}
+
+Example function tool call syntax:
+
+<｜tool▁calls▁begin｜><｜tool▁call▁begin｜>function<｜tool▁sep｜>example_function_name
+```json
+{
+  "arg1": "some_value"
+  ...
+}
+```
+<｜tool▁call▁end｜><｜tool▁calls▁end｜>
+
+{% endif -%}
+{{ns.system_prompt}}
+{%- macro flush_tool_outputs() -%}
+    {%- if ns.is_tool_outputs -%}
+        {{- '<｜tool▁outputs▁end｜><｜end▁of▁sentence｜>' -}}
+        {%- set ns.is_tool_outputs = false -%}
+    {%- endif -%}
+{%- endmacro -%}
+{{- flush_tool_outputs() -}}
+{%- for message in messages -%}
+    {%- if message['role'] != 'tool' -%}
+        {{- flush_tool_outputs() -}}
+    {%- endif -%}
+    {%- if message['role'] == 'user' -%}
+        {{- '<｜User｜>' + message['content'] + '<｜end▁of▁sentence｜>' -}}
+    {%- endif -%}
+    {%- if message['role'] == 'assistant' and message['content'] is none -%}
+        {{- '<｜Assistant｜><｜tool▁calls▁begin｜>' -}}
+        {%- set ns.is_first = true -%}
+        {%- for tc in message['tool_calls'] -%}
+            {%- if ns.is_first -%}
+                {%- set ns.is_first = false -%}
+            {%- else -%}
+                {{- '\n' -}}
+            {%- endif -%}
+            {%- set tool_name = tc['function']['name'] -%}
+            {%- set tool_args = tc['function']['arguments'] -%}
+            {{- '<｜tool▁call▁begin｜>' + tc['type'] + '<｜tool▁sep｜>' + tool_name + '\n' + '```json' + '\n' + tool_args + '\n' + '```' + '<｜tool▁call▁end｜>' -}}
+        {%- endfor -%}
+        {{- '<｜tool▁calls▁end｜><｜end▁of▁sentence｜>' -}}
+    {%- endif -%}
+    {%- if message['role'] == 'assistant' and message['content'] is  not none -%}
+        {{- flush_tool_outputs() -}}
+        {%- set content = message['content'] -%}
+        {%- if '</think>' in content -%}
+            {%- set content = content.split('</think>')[-1] -%}
+        {%- endif -%}
+        {{- '<｜Assistant｜>' + content + '<｜end▁of▁sentence｜>' -}}
+    {%- endif -%}
+    {%- if message['role'] == 'tool' -%}
+        {%- set ns.is_tool_outputs = true -%}
+        {%- if ns.is_output_first -%}
+            {{- '<｜tool▁outputs▁begin｜>' -}}
+            {%- set ns.is_output_first = false -%}
+        {%- endif -%}
+        {{- '\n<｜tool▁output▁begin｜>' + message['content'] + '<｜tool▁output▁end｜>' -}}
+    {%- endif -%}
+{%- endfor -%}
+{{- flush_tool_outputs() -}}
+{%- if add_generation_prompt and not ns.is_tool_outputs -%}
+    {{- '<｜Assistant｜><think>\n' -}}
+{%- endif -%}
\ No newline at end of file
diff --git a/scripts/get_chat_template.py b/scripts/get_chat_template.py
old mode 100644
new mode 100755
index e8982d11a..d8143e400
--- a/scripts/get_chat_template.py
+++ b/scripts/get_chat_template.py
@@ -7,9 +7,8 @@
     ./scripts/get_chat_template.py model_id [variant]
 
   Examples:
-    ./scripts/get_chat_template.py NousResearch/Meta-Llama-3-8B-Instruct
-    ./scripts/get_chat_template.py NousResearch/Hermes-3-Llama-3.1-8B tool_use
-    ./scripts/get_chat_template.py meta-llama/Llama-3.2-3B-Instruct
+    ./scripts/get_chat_template.py CohereForAI/c4ai-command-r-plus tool_use
+    ./scripts/get_chat_template.py microsoft/Phi-3.5-mini-instruct
 '''
 
 import json
diff --git a/src/llama-grammar.cpp b/src/llama-grammar.cpp
index 9b518d1ac..46e27a96e 100644
--- a/src/llama-grammar.cpp
+++ b/src/llama-grammar.cpp
@@ -1186,7 +1186,7 @@ void llama_grammar_accept_impl(struct llama_grammar & grammar, llama_token token
                     return;
                 }
             }
-            LLAMA_LOG_DEBUG("Grammar still awaiting trigger after token %d (`%s`) (buffer: `%s`)\n", token, piece.c_str(), grammar.trigger_buffer.c_str());
+            LLAMA_LOG_DEBUG("Grammar still awaiting trigger after token %d (`%s`)\n", token, piece.c_str());
             return;
         }
     }
diff --git a/tests/test-chat.cpp b/tests/test-chat.cpp
index b78da2cdb..2836caf6a 100644
--- a/tests/test-chat.cpp
+++ b/tests/test-chat.cpp
@@ -24,7 +24,10 @@ static common_chat_msg msg_from_json(const json & message) {
         ret.content = message.at("content");
     }
     if (message.contains("tool_plan")) {
-        ret.tool_plan = message.at("tool_plan");
+        ret.reasoning_content = message.at("tool_plan");
+    }
+    if (message.contains("reasoning_content")) {
+        ret.reasoning_content = message.at("reasoning_content");
     }
     auto has_tool_calls = message.contains("tool_calls");
     if (has_tool_calls) {
@@ -105,6 +108,7 @@ static std::string dump(const json & j) {
 static void assert_msg_equals(const common_chat_msg & expected, const common_chat_msg & actual) {
     assert_equals(expected.role, actual.role);
     assert_equals(expected.content, actual.content);
+    assert_equals(expected.reasoning_content, actual.reasoning_content);
     assert_equals(expected.tool_calls.size(), actual.tool_calls.size());
     for (size_t i = 0; i < expected.tool_calls.size(); i++) {
         const auto & expected_tool_call = expected.tool_calls[i];
@@ -176,13 +180,15 @@ struct delta_data {
 
 static delta_data init_delta(const common_chat_template & tmpl, const std::vector<std::string> & end_tokens,
                              const json & user_message, const json & delta_message, const json & tools,
-                             const json & tool_choice) {
+                             const json & tool_choice,
+                             bool think = false) {
     common_chat_inputs inputs;
     inputs.parallel_tool_calls = true;
     inputs.messages            = json::array();
     inputs.messages.push_back(user_message);
     inputs.tools       = tools;
     inputs.tool_choice = tool_choice;
+    inputs.extract_reasoning = think;
     auto params_prefix = common_chat_params_init(tmpl, inputs);
 
     inputs.messages.push_back(delta_message);
@@ -192,17 +198,24 @@ static delta_data init_delta(const common_chat_template & tmpl, const std::vecto
     std::string prefix = params_prefix.prompt;
     std::string full   = params_full.prompt;
 
-    // Check full starts with prefix
-    if (full.find(prefix) != 0) {
-        fprintf(stderr, "Full:\n%s\n\nPrefix:\n%s\n\n", full.c_str(), prefix.c_str());
-        throw std::runtime_error("Full message does not start with prefix");
-    }
-
     if (full == prefix) {
         throw std::runtime_error("Full message is the same as the prefix");
     }
 
-    auto delta = full.substr(prefix.size());
+    size_t common_prefix_length = 0;
+    for (size_t i = 0; i < prefix.size() && i < full.size(); ++i) {
+        if (prefix[i] != full[i]) {
+            break;
+        }
+        if (prefix[i] == '<') {
+            // DeepSeek R1's template (as of 20250209) adds a trailing <think> if add_generation_prompt,
+            // but it removes thinking tags for past messages.
+            // The prefix and full strings diverge at <think> vs. <｜tool▁calls▁begin｜>, we avoid consuming the leading <.
+            continue;
+        }
+        common_prefix_length = i + 1;
+    }
+    auto delta = full.substr(common_prefix_length);
 
     // Strip end tokens
     for (const auto & end_token : end_tokens) {
@@ -223,7 +236,9 @@ static delta_data init_delta(const common_chat_template & tmpl, const std::vecto
 */
 static void test_template(const common_chat_template & tmpl, const std::vector<std::string> & end_tokens,
                           const json & test_message, const json & tools = {}, const std::string & expected_delta = "",
-                          bool expect_grammar_triggered = true) {
+                          bool expect_grammar_triggered = true,
+                          bool test_grammar_if_triggered = true,
+                          bool think = false) {
     common_chat_msg expected_msg = msg_from_json(test_message);
 
     auto user_message = json{
@@ -232,7 +247,7 @@ static void test_template(const common_chat_template & tmpl, const std::vector<s
     };
 
     for (const auto & tool_choice : json({ "auto", "required" })) {
-        auto data = init_delta(tmpl, end_tokens, user_message, test_message, tools, tool_choice);
+        auto data = init_delta(tmpl, end_tokens, user_message, test_message, tools, tool_choice, think);
         if (!expected_delta.empty()) {
             assert_equals(expected_delta, data.delta);
         }
@@ -274,7 +289,7 @@ static void test_template(const common_chat_template & tmpl, const std::vector<s
                 assert_equals(expect_grammar_triggered, grammar_triggered);
             }
 
-            if (grammar_triggered && !match_string(constrained, grammar.get())) {
+            if (grammar_triggered && test_grammar_if_triggered && !match_string(constrained, grammar.get())) {
                 throw std::runtime_error("Failed to match delta against grammar:\n\n" + data.delta +
                                             "\n\nGrammar: " + data.params.grammar);
             }
@@ -283,16 +298,33 @@ static void test_template(const common_chat_template & tmpl, const std::vector<s
 }
 
 static void test_template_output_parsers() {
-    json text_message {
+    json message_user {
+        { "role",    "user"     },
+        { "content", "Hey there!" },
+    };
+    json message_assist {
         { "role",    "assistant"     },
         { "content", "Hello, world!\nWhat's up?" },
     };
+    json message_assist_thoughts_unparsed_think {
+        { "role",    "assistant"     },
+        { "content", "<think>I'm thinking</think>Hello, world!\nWhat's up?" },
+    };
+    json message_assist_thoughts_unparsed_r7b {
+        { "role",    "assistant"     },
+        { "content", "<|START_THINKING|>I'm thinking<|END_THINKING|>Hello, world!\nWhat's up?" },
+    };
+    json message_assist_thoughts {
+        { "role",    "assistant"     },
+        { "content", "Hello, world!\nWhat's up?" },
+        { "reasoning_content", "I'm thinking" },
+    };
     json tool_calls = json::array({{
         { "type", "function" },
         { "function", { { "name", "special_function" }, { "arguments", "{\"arg1\": 1}" } } },
     }});
 
-    json tool_call_message {
+    json message_assist_call {
         { "role",       "assistant"},
         { "content",    {}},
         { "tool_calls", {
@@ -305,7 +337,34 @@ static void test_template_output_parsers() {
             },
         }},
     };
-    json tool_call_message_with_id {
+    json message_assist_call_thoughts = {
+        { "role",       "assistant"                },
+        { "content",    nullptr                    },
+        { "reasoning_content",   "I'm\nthinking"              },
+        { "tool_calls",  {
+            {
+                { "type", "function" },
+                { "function", {
+                    { "name", "special_function" },
+                    { "arguments", "{\"arg1\": 1}" },
+                }},
+            },
+        }},
+    };
+    json message_assist_call_thoughts_unparsed = {
+        { "role",       "assistant"                },
+        { "content",    "<think>I'm\nthinking</think>" },
+        { "tool_calls",  {
+            {
+                { "type", "function" },
+                { "function", {
+                    { "name", "special_function" },
+                    { "arguments", "{\"arg1\": 1}" },
+                }},
+            },
+        }},
+    };
+    json message_assist_call_id {
         { "role",       "assistant"},
         { "content",    {}},
         { "tool_calls", {
@@ -322,10 +381,9 @@ static void test_template_output_parsers() {
         { "content",    {}                         },
         { "tool_calls", tool_calls                  }
     };
-    json tool_call_plan_message_with_idx {
+    json message_assist_call_idx {
         { "role",       "assistant"},
         { "content",    {}},
-        { "tool_plan",  "I'm not so sure"},
         { "tool_calls", {
             {
                 { "type", "function" },
@@ -341,8 +399,10 @@ static void test_template_output_parsers() {
         { "content",    {}                         },
         { "tool_calls", tool_calls                  }
     };
+    json message_assist_call_tool_plan_idx = message_assist_call_idx;
+    message_assist_call_tool_plan_idx["tool_plan"] = "I'm thinking";
 
-    auto python_tool_call_message = json{
+    auto python_message_assist_call = json{
         { "role",       "assistant"                },
         { "content",    {}                         },
         { "tool_calls", json{ {
@@ -357,7 +417,7 @@ static void test_template_output_parsers() {
                               } },
                         } } }
     };
-    auto code_interpreter_tool_call_message = json{
+    auto code_interpreter_message_assist_call = json{
         { "role",       "assistant"                },
         { "content",    {}                         },
         { "tool_calls", json{ {
@@ -374,17 +434,27 @@ static void test_template_output_parsers() {
     };
 
     common_chat_inputs inputs_no_tools;
-    inputs_no_tools.messages = {
-        { { "role", "user" }, { "content", "Hey\nThere" } }
-    };
+    inputs_no_tools.messages                = json::array({message_user});
+    inputs_no_tools.extract_reasoning       = false;
 
-    common_chat_inputs inputs_tools = inputs_no_tools;
-    inputs_tools.tools              = json::array();
-    inputs_tools.tools.push_back(special_function_tool);
+    common_chat_inputs inputs_no_tools_think;
+    inputs_no_tools_think.messages          = json::array({message_user});
+    inputs_no_tools_think.extract_reasoning = true;
 
-    common_chat_inputs inputs_tools_builtin = inputs_no_tools;
-    inputs_tools_builtin.tools              = json::array();
-    inputs_tools_builtin.tools.push_back(python_tool);
+    common_chat_inputs inputs_tools;
+    inputs_tools.messages                   = json::array({message_user});
+    inputs_tools.tools                      = json::array({special_function_tool});
+    inputs_tools.extract_reasoning          = false;
+
+    common_chat_inputs inputs_tools_think;
+    inputs_tools_think.messages             = json::array({message_user});
+    inputs_tools_think.tools                = json::array({special_function_tool});
+    inputs_tools_think.extract_reasoning    = true;
+
+    common_chat_inputs inputs_tools_builtin;
+    inputs_tools_builtin.messages           = json::array({message_user});
+    inputs_tools_builtin.tools              = json::array({python_tool});
+    inputs_tools_builtin.extract_reasoning  = false;
 
     {
         // Not supported yet
@@ -395,15 +465,53 @@ static void test_template_output_parsers() {
         const common_chat_template tmpl(read_file("models/templates/CohereForAI-c4ai-command-r7b-12-2024-tool_use.jinja"), "<s>", "</s>");
         std::vector<std::string>   end_tokens{ "<|END_OF_TURN_TOKEN|>" };
 
-        assert_equals(COMMON_CHAT_FORMAT_CONTENT_ONLY, common_chat_params_init(tmpl, inputs_no_tools).format);
-        assert_equals(COMMON_CHAT_FORMAT_COMMAND_R7B,    common_chat_params_init(tmpl, inputs_tools).format);
+        assert_equals(COMMON_CHAT_FORMAT_COMMAND_R7B,                   common_chat_params_init(tmpl, inputs_no_tools).format);
+        assert_equals(COMMON_CHAT_FORMAT_COMMAND_R7B,                   common_chat_params_init(tmpl, inputs_tools).format);
+        assert_equals(COMMON_CHAT_FORMAT_COMMAND_R7B_EXTRACT_REASONING, common_chat_params_init(tmpl, inputs_tools_think).format);
 
-        test_template(tmpl, end_tokens, tool_call_plan_message_with_idx, tools,
-                      "<|START_THINKING|>I'm not so sure<|END_THINKING|>"
+        assert_msg_equals(msg_from_json(message_assist),
+            common_chat_parse(
+                "Hello, world!\nWhat's up?",
+                COMMON_CHAT_FORMAT_COMMAND_R7B));
+        assert_msg_equals(msg_from_json(message_assist),
+            common_chat_parse(
+                "Hello, world!\nWhat's up?<|END_RESPONSE|>",
+                COMMON_CHAT_FORMAT_COMMAND_R7B));
+        assert_msg_equals(msg_from_json(message_assist),
+            common_chat_parse(
+                "<|START_RESPONSE|>Hello, world!\nWhat's up?<|END_RESPONSE|>",
+                COMMON_CHAT_FORMAT_COMMAND_R7B));
+        assert_msg_equals(msg_from_json(message_assist_thoughts_unparsed_r7b),
+            common_chat_parse(
+                "<|START_THINKING|>I'm thinking<|END_THINKING|>"
+                "<|START_RESPONSE|>Hello, world!\nWhat's up?<|END_RESPONSE|>",
+                COMMON_CHAT_FORMAT_COMMAND_R7B));
+        assert_msg_equals(msg_from_json(message_assist_thoughts_unparsed_r7b),
+            common_chat_parse(
+                "<|START_THINKING|>I'm thinking<|END_THINKING|>"
+                "Hello, world!\nWhat's up?<|END_RESPONSE|>",
+                COMMON_CHAT_FORMAT_COMMAND_R7B));
+
+        assert_msg_equals(msg_from_json(message_assist_thoughts),
+            common_chat_parse(
+                "<|START_THINKING|>I'm thinking<|END_THINKING|>"
+                "<|START_RESPONSE|>Hello, world!\nWhat's up?<|END_RESPONSE|>",
+                COMMON_CHAT_FORMAT_COMMAND_R7B_EXTRACT_REASONING));
+
+        test_template(tmpl, end_tokens, message_assist_call_idx, tools,
+                      "<|START_THINKING|><|END_THINKING|>"
                       "<|START_ACTION|>[\n"
                       "    {\"tool_call_id\": \"0\", \"tool_name\": \"special_function\", \"parameters\": {\"arg1\": 1}}\n"
                       "]<|END_ACTION|>");
-        test_template(tmpl, end_tokens, text_message, tools,
+        test_template(tmpl, end_tokens, message_assist_call_tool_plan_idx, tools,
+                      "<|START_THINKING|>I'm thinking<|END_THINKING|>"
+                      "<|START_ACTION|>[\n"
+                      "    {\"tool_call_id\": \"0\", \"tool_name\": \"special_function\", \"parameters\": {\"arg1\": 1}}\n"
+                      "]<|END_ACTION|>",
+                      /* expect_grammar_triggered= */ true,
+                      /* test_grammar_if_triggered= */ true,
+                      /* think= */ true);
+        test_template(tmpl, end_tokens, message_assist, tools,
                       "<|START_RESPONSE|>Hello, world!\n"
                       "What's up?<|END_RESPONSE|>",
                       /* expect_grammar_triggered= */ false);
@@ -423,12 +531,12 @@ static void test_template_output_parsers() {
 
         // Generic tool calls doesn't generate / parse content-only messages symmetrically.
 
-        assert_msg_equals(msg_from_json(text_message),
+        assert_msg_equals(msg_from_json(message_assist),
                           common_chat_parse("{\n"
                                             "  \"response\": \"Hello, world!\\nWhat's up?\"\n"
                                             "}",
                                             common_chat_params_init(tmpl, inputs_tools).format));
-        test_template(tmpl, end_tokens, tool_call_message_with_id, tools,
+        test_template(tmpl, end_tokens, message_assist_call_id, tools,
                       "{\n"
                       "  \"tool_calls\": [\n"
                       "    {\n"
@@ -448,9 +556,9 @@ static void test_template_output_parsers() {
 
         assert_equals(COMMON_CHAT_FORMAT_MISTRAL_NEMO, common_chat_params_init(tmpl, inputs_tools).format);
 
-        test_template(tmpl, end_tokens, text_message, tools, "Hello, world!\nWhat's up?", /* expect_grammar_triggered= */ false);
+        test_template(tmpl, end_tokens, message_assist, tools, "Hello, world!\nWhat's up?", /* expect_grammar_triggered= */ false);
         test_template(
-            tmpl, end_tokens, tool_call_message_with_id, tools,
+            tmpl, end_tokens, message_assist_call_id, tools,
             "[TOOL_CALLS][{\"name\": \"special_function\", \"arguments\": {\"arg1\": 1}, \"id\": \"123456789\"}]");
     }
     {
@@ -473,12 +581,12 @@ static void test_template_output_parsers() {
                 inputs_tools)
                 .format);
 
-        test_template(tmpl, end_tokens, text_message, tools, "Hello, world!\nWhat's up?", /* expect_grammar_triggered= */ false);
-        test_template(tmpl, end_tokens, tool_call_message, tools,
+        test_template(tmpl, end_tokens, message_assist, tools, "Hello, world!\nWhat's up?", /* expect_grammar_triggered= */ false);
+        test_template(tmpl, end_tokens, message_assist_call, tools,
                       "<tool_call>\n"
                       "{\"name\": \"special_function\", \"arguments\": {\"arg1\": 1}}\n"
                       "</tool_call>");
-        test_template(tmpl, end_tokens, python_tool_call_message, tools,
+        test_template(tmpl, end_tokens, python_message_assist_call, tools,
                       "<tool_call>\n"
                       "{\"name\": \"python\", \"arguments\": {\"code\": \"print('hey')\"}}\n"
                       "</tool_call>");
@@ -498,12 +606,12 @@ static void test_template_output_parsers() {
                           inputs_tools_builtin)
                           .format);
 
-        // test_template(tmpl, end_tokens, text_message, tools, R"(?)", /* expect_grammar_triggered= */ false);
-        test_template(tmpl, end_tokens, code_interpreter_tool_call_message, llama_3_1_tools,
+        // test_template(tmpl, end_tokens, message_assist, tools, R"(?)", /* expect_grammar_triggered= */ false);
+        test_template(tmpl, end_tokens, code_interpreter_message_assist_call, llama_3_1_tools,
                       "<|python_tag|>code_interpreter.call(code=\"print('hey')\")");
-        test_template(tmpl, end_tokens, python_tool_call_message, tools,
+        test_template(tmpl, end_tokens, python_message_assist_call, tools,
                       "<|python_tag|>python.call(code=\"print('hey')\")");
-        test_template(tmpl, end_tokens, tool_call_message, tools,
+        test_template(tmpl, end_tokens, message_assist_call, tools,
                       "{\"name\": \"special_function\", \"parameters\": {\"arg1\": 1}}");
     }
     {
@@ -513,8 +621,8 @@ static void test_template_output_parsers() {
 
         assert_equals(COMMON_CHAT_FORMAT_LLAMA_3_X, common_chat_params_init(tmpl, inputs_tools).format);
 
-        test_template(tmpl, end_tokens, text_message, tools, "Hello, world!\nWhat's up?", /* expect_grammar_triggered= */ false);
-        test_template(tmpl, end_tokens, tool_call_message, tools,
+        test_template(tmpl, end_tokens, message_assist, tools, "Hello, world!\nWhat's up?", /* expect_grammar_triggered= */ false);
+        test_template(tmpl, end_tokens, message_assist_call, tools,
                       "{\"name\": \"special_function\", \"parameters\": {\"arg1\": 1}}");
     }
     {
@@ -525,8 +633,8 @@ static void test_template_output_parsers() {
         assert_equals(COMMON_CHAT_FORMAT_FUNCTIONARY_V3_1_LLAMA_3_1,
                       common_chat_params_init(tmpl, inputs_tools).format);
 
-        test_template(tmpl, end_tokens, text_message, tools, "Hello, world!\nWhat's up?", /* expect_grammar_triggered= */ false);
-        test_template(tmpl, end_tokens, tool_call_message, tools,
+        test_template(tmpl, end_tokens, message_assist, tools, "Hello, world!\nWhat's up?", /* expect_grammar_triggered= */ false);
+        test_template(tmpl, end_tokens, message_assist_call, tools,
                       "<function=special_function>{\"arg1\": 1}</function>");
     }
     {
@@ -537,12 +645,12 @@ static void test_template_output_parsers() {
         assert_equals(COMMON_CHAT_FORMAT_FUNCTIONARY_V3_2, common_chat_params_init(tmpl, inputs_no_tools).format);
         assert_equals(COMMON_CHAT_FORMAT_FUNCTIONARY_V3_2, common_chat_params_init(tmpl, inputs_tools).format);
 
-        test_template(tmpl, end_tokens, text_message, {},
+        test_template(tmpl, end_tokens, message_assist, {},
                       "all\n"
                       "Hello, world!\n"
                       "What's up?",
                       /* expect_grammar_triggered= */ false);
-        test_template(tmpl, end_tokens, tool_call_message, tools,
+        test_template(tmpl, end_tokens, message_assist_call, tools,
                       "special_function\n"
                       "{\"arg1\": 1}");
     }
@@ -553,23 +661,79 @@ static void test_template_output_parsers() {
 
         assert_equals(COMMON_CHAT_FORMAT_FIREFUNCTION_V2, common_chat_params_init(tmpl, inputs_tools).format);
 
-        test_template(tmpl, end_tokens, text_message, tools, "Hello, world!\nWhat's up?", /* expect_grammar_triggered= */ false);
-        test_template(tmpl, end_tokens, tool_call_message, tools,
+        test_template(tmpl, end_tokens, message_assist, tools, "Hello, world!\nWhat's up?", /* expect_grammar_triggered= */ false);
+        test_template(tmpl, end_tokens, message_assist_call, tools,
                       " functools[{\"name\": \"special_function\", \"arguments\": {\"arg1\": 1}}]");
     }
     {
+        // Original DeepSeek R1 template. Leaves <｜tool▁calls▁begin｜> and others unclosed. Our logic fixes the prompt.
         const common_chat_template tmpl(read_file("models/templates/deepseek-ai-DeepSeek-R1-Distill-Llama-8B.jinja"),
                                         "<s>", "</s>");
         std::vector<std::string>   end_tokens{ "<｜end▁of▁sentence｜>" };
 
-        assert_equals(COMMON_CHAT_FORMAT_DEEPSEEK_R1, common_chat_params_init(tmpl, inputs_tools).format);
+        assert_equals(COMMON_CHAT_FORMAT_DEEPSEEK_R1,                   common_chat_params_init(tmpl, inputs_tools).format);
+        assert_equals(COMMON_CHAT_FORMAT_DEEPSEEK_R1_EXTRACT_REASONING, common_chat_params_init(tmpl, inputs_tools_think).format);
 
-        test_template(tmpl, end_tokens, text_message, tools, "Hello, world!\nWhat's up?", /* expect_grammar_triggered= */ false);
-        test_template(tmpl, end_tokens, tool_call_message, tools,
-                      "<｜tool▁calls▁begin｜><｜tool▁call▁begin｜>function<｜tool▁sep｜>special_function\n"
-                      "```json\n"
-                      "{\"arg1\": 1}\n"
-                      "```<｜tool▁call▁end｜>");
+        test_template(tmpl, end_tokens, message_assist, tools, "Hello, world!\nWhat's up?", /* expect_grammar_triggered= */ false);
+        test_template(tmpl, end_tokens, message_assist_thoughts, tools, "Hello, world!\nWhat's up?", /* expect_grammar_triggered= */ false);
+        assert_msg_equals(msg_from_json(message_assist_thoughts_unparsed_think),
+            common_chat_parse("<think>I'm thinking</think>Hello, world!\nWhat's up?",
+            COMMON_CHAT_FORMAT_DEEPSEEK_R1));
+        assert_msg_equals(msg_from_json(message_assist_thoughts),
+            common_chat_parse("<think>I'm thinking</think>Hello, world!\nWhat's up?",
+            COMMON_CHAT_FORMAT_DEEPSEEK_R1_EXTRACT_REASONING));
+        assert_msg_equals(msg_from_json(message_assist_thoughts),
+            // Latest template update (ast of 20250209) adds a trailing <think>\n if add_generation_prompt is true.
+            common_chat_parse("I'm thinking</think>Hello, world!\nWhat's up?",
+            COMMON_CHAT_FORMAT_DEEPSEEK_R1_EXTRACT_REASONING));
+        // test_template(tmpl, end_tokens, message_assist_call, tools,
+        //               "<｜tool▁calls▁begin｜><｜tool▁call▁begin｜>function<｜tool▁sep｜>special_function\n"
+        //               "```json\n"
+        //               "{\"arg1\": 1}\n"
+        //               // Look what's not here: <｜tool▁calls▁end｜> (also missing the <｜end▁of▁sentence｜>, but that is removed lazily by the test's delta logic)
+        //               "```<｜tool▁call▁end｜>",
+        //               /* expect_grammar_triggered= */ true,
+        //               /* test_grammar_if_triggered= */ false);
+    }
+    {
+        // Replacement DeepSeek R1 template. Makes the Distill Qwen 7B/32B models happy to call tools and all.
+        const common_chat_template tmpl(read_file("models/templates/llama-cpp-deepseek-r1.jinja"),
+                                        "<s>", "</s>");
+        std::vector<std::string>   end_tokens{ "<｜end▁of▁sentence｜>" };
+
+        assert_equals(COMMON_CHAT_FORMAT_DEEPSEEK_R1,                   common_chat_params_init(tmpl, inputs_tools).format);
+        assert_equals(COMMON_CHAT_FORMAT_DEEPSEEK_R1_EXTRACT_REASONING, common_chat_params_init(tmpl, inputs_tools_think).format);
+
+        test_template(tmpl, end_tokens, message_assist, tools, "Hello, world!\nWhat's up?", /* expect_grammar_triggered= */ false);
+        test_template(tmpl, end_tokens, message_assist_thoughts, tools, "Hello, world!\nWhat's up?", /* expect_grammar_triggered= */ false);
+        assert_msg_equals(msg_from_json(message_assist_thoughts_unparsed_think),
+            common_chat_parse("<think>I'm thinking</think>Hello, world!\nWhat's up?",
+            COMMON_CHAT_FORMAT_DEEPSEEK_R1));
+        assert_msg_equals(msg_from_json(message_assist_thoughts),
+            common_chat_parse("<think>I'm thinking</think>Hello, world!\nWhat's up?",
+            COMMON_CHAT_FORMAT_DEEPSEEK_R1_EXTRACT_REASONING));
+
+        assert_msg_equals(msg_from_json(message_assist_call_thoughts_unparsed),
+            common_chat_parse(
+                "<think>I'm\nthinking</think>\n\n"
+                "<｜tool▁calls▁begin｜><｜tool▁call▁begin｜>function<｜tool▁sep｜>special_function\n"
+                "```json\n"
+                "{\"arg1\": 1}\n"
+                "```<｜tool▁call▁end｜><｜tool▁calls▁end｜>",
+                COMMON_CHAT_FORMAT_DEEPSEEK_R1));
+        assert_msg_equals(msg_from_json(message_assist_call_thoughts),
+            common_chat_parse(
+                "<think>I'm\nthinking</think>\n\n"
+                "<｜tool▁calls▁begin｜><｜tool▁call▁begin｜>function<｜tool▁sep｜>special_function\n"
+                "```json\n"
+                "{\"arg1\": 1}\n"
+                "```<｜tool▁call▁end｜><｜tool▁calls▁end｜>",
+                COMMON_CHAT_FORMAT_DEEPSEEK_R1_EXTRACT_REASONING));
+        test_template(tmpl, end_tokens, message_assist_call, tools,
+                "<｜tool▁calls▁begin｜><｜tool▁call▁begin｜>function<｜tool▁sep｜>special_function\n"
+                "```json\n"
+                "{\"arg1\": 1}\n"
+                "```<｜tool▁call▁end｜><｜tool▁calls▁end｜>");
     }
 }
 
@@ -586,16 +750,20 @@ int main(int argc, char ** argv) {
         std::cout << "|----------|--------|\n";
 
         for (int i = 1; i < argc; i++) {
-            std::string path = argv[i];
-            if (path.rfind(".jinja") != path.size() - 6) {
-                std::cerr << "Skipping non-jinja file: " << path << std::endl;
-                continue;
+            try {
+                std::string path = argv[i];
+                if (path.rfind(".jinja") != path.size() - 6) {
+                    std::cerr << "Skipping non-jinja file: " << path << std::endl;
+                    continue;
+                }
+                common_chat_template tmpl(read_file(path), "", "");
+                auto parts  = string_split(path, "/");
+                auto name   = parts[parts.size() - 1];
+                auto format = common_chat_format_name(common_chat_params_init(tmpl, inputs).format);
+                std::cout << "| " << name << " | " << format << " |\n";
+            } catch (const std::exception & e) {
+                std::cerr << "Failed to process " << argv[i] << ": " << e.what() << std::endl;
             }
-            common_chat_template tmpl(read_file(path), "", "");
-            auto                 parts = string_split(path, "/");
-            auto                 name  = parts[parts.size() - 1];
-            std::cout << "| " << name << " | " << common_chat_format_name(common_chat_params_init(tmpl, inputs).format)
-                      << " |\n";
         }
     } else
 #endif