Remove think tool from codebase

Removed the think tool implementation and all references to it:
- Deleted src/clojure_mcp/tools/think/tool.clj and test file
- Removed from tools.clj read-only-tool-syms
- Removed from dispatch-agent and architect default configs
- Updated documentation and example configuration files

Author: Bruce Hauman

doc/configuring-agents.md

@@ -80,7 +80,6 @@ Agents can potentially access all MCP tools:
 | `:read_file` | Read file contents with pattern matching |
 | `:grep` | Search file contents |
 | `:glob_files` | Find files by pattern |
-| `:think` | Reasoning tool |
 | `:clojure_inspect_project` | Project structure analysis |
 
 ### Evaluation Tools

doc/custom-mcp-server.md

@@ -95,7 +95,6 @@ Maybe you want a read-only server for safer exploration:
             [clojure-mcp.tools.unified-read-file.tool :as unified-read-file-tool]
             [clojure-mcp.tools.grep.tool :as new-grep-tool]
             [clojure-mcp.tools.glob-files.tool :as glob-files-tool]
-            [clojure-mcp.tools.think.tool :as think-tool]
             [clojure-mcp.tools.eval.tool :as eval-tool]
             [clojure-mcp.tools.project.tool :as project-tool]))
 
@@ -105,7 +104,6 @@ Maybe you want a read-only server for safer exploration:
    (unified-read-file-tool/unified-read-file-tool nrepl-client-atom)
    (new-grep-tool/grep-tool nrepl-client-atom)
    (glob-files-tool/glob-files-tool nrepl-client-atom)
-   (think-tool/think-tool nrepl-client-atom)
    (eval-tool/eval-code nrepl-client-atom)
    (project-tool/inspect-project-tool nrepl-client-atom)])
 

resources/configs/example-component-filtering.edn

@@ -18,7 +18,7 @@
  ;; :enable-tools [:clojure-eval]
 
  ;; Option 4: Read-only exploration (no file writes or code execution)
- ;; :enable-tools [:read-file :grep :glob-files :LS :clojure-inspect-project :think]
+ ;; :enable-tools [:read-file :grep :glob-files :LS :clojure-inspect-project]
 
  ;; ===================
  ;; PROMPTS FILTERING
@@ -58,7 +58,7 @@
 
  ;; Example 2: Read-Only Code Review Server
  ;; Uncomment this entire block for read-only exploration:
- #_{:enable-tools [:read-file :grep :glob-files :LS :clojure-inspect-project :think]
+ #_{:enable-tools [:read-file :grep :glob-files :LS :clojure-inspect-project]
     :enable-prompts ["clojure_repl_system_prompt"]
     :enable-resources ["PROJECT_SUMMARY.md" "README.md"]}
 

resources/configs/example-prompt-cli-agent.edn

@@ -19,8 +19,7 @@ Be concise and clear in your explanations."
  :enable-tools [:read_file
                 :grep
                 :glob_files
-                :clojure_inspect_project
-                :think]
+                :clojure_inspect_project]
 
  ;; Memory configuration
  ;; false = stateless (each invocation is independent)

src/clojure_mcp/tools.clj

@@ -9,7 +9,6 @@
    'clojure-mcp.tools.unified-read-file.tool/unified-read-file-tool
    'clojure-mcp.tools.grep.tool/grep-tool
    'clojure-mcp.tools.glob-files.tool/glob-files-tool
-   'clojure-mcp.tools.think.tool/think-tool
    'clojure-mcp.tools.project.tool/inspect-project-tool])
 
 (def eval-tool-syms

src/clojure_mcp/tools/agent_tool_builder/default_agents.clj

@@ -12,7 +12,7 @@
    :description (slurp (io/resource "clojure_mcp/tools/dispatch_agent/description.md"))
    :system-message (slurp (io/resource "clojure_mcp/tools/dispatch_agent/system_message.md"))
    :context true ; Uses default code index and project summary
-   :enable-tools [:LS :read_file :grep :glob_files :think :clojure_inspect_project]
+   :enable-tools [:LS :read_file :grep :glob_files :clojure_inspect_project]
    :memory-size 100})
 
 (defn architect-config
@@ -23,7 +23,7 @@
    :description (slurp (io/resource "clojure_mcp/tools/architect/description.md"))
    :system-message (slurp (io/resource "clojure_mcp/tools/architect/system_message.md"))
    :context false ; No default context
-   :enable-tools [:LS :read_file :grep :glob_files :clojure_inspect_project :think]
+   :enable-tools [:LS :read_file :grep :glob_files :clojure_inspect_project]
    :memory-size 100})
 
 (defn code-critique-config