edit new scratch_pad persistence functionality

Author: Bruce Hauman

PROJECT_SUMMARY.md

@@ -62,8 +62,8 @@ The project allows AI assistants to:
 - `/src/clojure_mcp/tools/architect/`: Technical planning and architecture assistance
 - `/src/clojure_mcp/tools/scratch_pad/`: Persistent scratch pad for inter-tool communication
   - `core.clj`: Core functionality for data storage and retrieval
-  - `tool.clj`: MCP integration with path-based operations (set_path, get_path, delete_path, persistence_config, status)
-  - `config.clj`: Configuration file management for dual-mode persistence (config file + runtime tool)
+  - `tool.clj`: MCP integration with path-based operations (set_path, get_path, delete_path)
+  - `config.clj`: Configuration file management for persistence
   - `truncate.clj`: Pretty-printing with depth truncation
 
 #### Unused Tools (moved to other_tools/)
@@ -150,11 +150,9 @@ your-project/
 - `scratch-pad-load`: Boolean flag to enable/disable scratch pad persistence (default: `false`)
   - `true` - Loads existing data on startup and saves changes to disk
   - `false` - Scratch pad operates in memory only, no file persistence
-  - Can be configured via config file OR runtime using `persistence_config` operation
 - `scratch-pad-file`: Filename for scratch pad persistence (default: `"scratch_pad.edn"`)
   - Specifies the filename within `.clojure-mcp/` directory
   - Only used when `scratch-pad-load` is `true`
-  - Can be modified at runtime using `persistence_config` operation
 
 ### Example Configuration
 ```edn
@@ -220,7 +218,7 @@ The following tools are available in the default configuration (`main.clj`):
 
 | Tool Name | Description | Example Usage |
 |-----------|-------------|---------------|
-| `scratch_pad` | A persistent scratch pad for storing structured data between tool calls | Task tracking, intermediate results, inter-agent communication, with dual-mode persistence configuration |
+| `scratch_pad` | A persistent scratch pad for storing structured data between tool calls | Task tracking, intermediate results, inter-agent communication |
 | `code_critique` | Starts an interactive code review conversation that provides constructive feedback on your Clojure code | Iterative code quality improvement |
 
 ## Tool Examples
@@ -283,18 +281,6 @@ scratch_pad:
   path: ["todos", 0]
   explanation: Checking first task
   Output: Value at ["todos", 0]: {task: "Write tests", done: false}
-
-scratch_pad:
-  op: persistence_config
-  enabled: true
-  filename: "my_workspace.edn"
-  explanation: Enable persistence with custom filename
-  Output: Persistence enabled (file: my_workspace.edn)
-
-scratch_pad:
-  op: status
-  explanation: Check persistence status
-  Output: Scratch Pad Status with file info, size, and entry count
 ```
 
 ## Architecture and Design Patterns
@@ -363,13 +349,8 @@ scratch_pad:
    - Path elements as arrays of strings and numbers
    - Tree visualization for debugging and inspection
    - Pretty-printed output with truncation at depth 3 for readability
-   - Dual-mode persistence configuration:
-     - **Config File Based**: Enable persistence via `.clojure-mcp/config.edn` file
-     - **Runtime Tool Based**: Use `persistence_config` operation to enable/disable and configure filename
-     - Tool-based changes automatically update config file for session persistence
-   - Lock file management to prevent data corruption from multiple instances
+   - **Config File Based**: Enable persistence via `.clojure-mcp/config.edn` file
    - Error handling for corrupted files with user notification
-   - Status operation showing persistence state, file info, and statistics
 
 ## Development Workflow Recommendations
 
@@ -392,7 +373,6 @@ scratch_pad:
      - Storing intermediate computation results
      - Building up complex data structures incrementally
      - Sharing context between different agents or tool calls
-     - Enable persistence via config file or `persistence_config` operation for data that should survive sessions
 
 4. **Logging System**:
    - Uses `clojure.tools.logging` with Logback backend
@@ -495,9 +475,6 @@ See `/doc/custom-mcp-server.md` for comprehensive documentation on creating cust
 - Building complex data structures incrementally
 - Path-based data manipulation using `set_path`/`get_path`/`delete_path` operations
 - Direct storage of JSON-compatible values
-- **Dual-mode persistence configuration**: Configure persistence via config file OR runtime tool operations
-- Runtime configuration operations (`persistence_config`, `status`) with immediate effect
-- Automatic config file updates when using tool-based configuration
 
 **Tool Reorganization**: To improve codebase maintainability, unused tools have been moved to `/src/clojure_mcp/other_tools/`. This separation clarifies which tools are actively used in the main MCP server (`main.clj`) versus those that remain available but are not currently essential.
 

README.md

@@ -44,7 +44,7 @@ it is.
 
 ## The Good News
 
-There is a story that Clojure developers you may have come to believe. The
+There is a story that Clojure developers may have come to believe. The
 story that LLMs are overwhelmingly trained on more mainstream
 languages and as a result those languages have the upper hand when it
 comes to LLM assisted coding. I'm here to tell you that this is just
@@ -658,7 +658,6 @@ The default tools included in `main.clj` are organized by category to support di
 - **Persistent Workspace**: Store structured data for planning and inter-tool communication
 - **Memory-Only by Default**: Data is stored in memory only and lost when session ends (default behavior)
 - **Optional File Persistence**: Enable to save data between sessions and server restarts
-- **Dual-Mode Configuration**: Configure persistence via config file or runtime tool operations
 - **Path-Based Operations**: Use `set_path`, `get_path`, `delete_path` for precise data manipulation
 - **JSON Compatibility**: Store any JSON-compatible data (objects, arrays, strings, numbers, booleans)
 
@@ -667,28 +666,6 @@ By default, the scratch pad operates in memory only. Data persists during the se
 
 **Enabling Persistence:**
 
-Option 1 - Runtime Configuration (Immediate Effect):
-```
-# Enable persistence via tool operation
-scratch_pad:
-  op: persistence_config
-  enabled: true
-  filename: "my_workspace.edn"  # optional, defaults to "scratch_pad.edn"
-  explanation: Enable persistence with custom filename
-
-# Check persistence status
-scratch_pad:
-  op: status
-  explanation: Check current persistence settings
-
-# Disable persistence (data remains in memory)
-scratch_pad:
-  op: persistence_config
-  enabled: false
-  explanation: Disable file persistence
-```
-
-Option 2 - Configuration File (On Startup):
 Add to `.clojure-mcp/config.edn`:
 ```edn
 {:scratch-pad-load true    ; false by default
@@ -699,9 +676,6 @@ Add to `.clojure-mcp/config.edn`:
 - Files are saved in `.clojure-mcp/` directory within your project
 - Changes are automatically saved when persistence is enabled
 - Corrupted files are handled gracefully with error reporting
-- Runtime configuration updates the config file for persistence across restarts
-
-
 
 ## 🔧 Customization
 
@@ -780,7 +754,7 @@ Boolean flag to control bash command execution mode (default: `true`). This sett
 - `false` - Useful when the nREPL server is not a Clojure process, i.e. CLJS, Babashka, Scittle
 
 **Technical details:**
-- When `true`, bash commands run in a separate nREPL session to prevent interference with your REPL state
+- When `true`, bash commands run in a separate nREPL session
 - Both modes apply consistent output truncation (8500 chars total, split between stdout/stderr)
 - Local execution may be faster for simple commands but requires the MCP server to have necessary tools installed
 
@@ -810,16 +784,11 @@ Boolean flag to enable/disable scratch pad persistence on startup (default: `fal
 - `false` - Best for temporary planning and session-only data
 - `true` - When you want data to persist across sessions and server restarts
 
-**Note:** This setting controls persistence at startup. You can also enable/disable persistence at runtime using the `persistence_config` operation.
-
 #### `scratch-pad-file`
 Filename for scratch pad persistence (default: `"scratch_pad.edn"`).
 
 **Configuration:**
 - Specifies the filename within `.clojure-mcp/` directory
-- Only used when `scratch-pad-load` is `true`
-- Can be modified at runtime using `persistence_config` operation
-- Runtime changes are saved to the config file for future sessions
 
 ### Example Configuration