docs: update all references from codeprism-mcp-server to codeprism binary

Comprehensive update to align all documentation, test specs, and examples
with the new binary name 'codeprism':

Configuration Updates:
- Update test-harness.yaml and test-harness-fixed.yaml to use 'codeprism --mcp'
- Update codeprism-moth-specs to use correct binary and args
- Update comprehensive test files to spawn correct binary

Documentation Updates:
- README.md: Update all examples to use 'codeprism' with --mcp flag
- Update download URLs to reflect new binary naming (codeprism-*)
- Update Claude Desktop config examples with proper args structure
- docs/: Update all command examples across documentation

Docusaurus Documentation:
- Update all .md files in codeprism-docs/ to use 'codeprism --mcp'
- Update configuration examples in getting-started guides
- Update tools documentation and integration examples

Behavioral Note:
- SERVER_NAME constant kept as 'codeprism-mcp-server' for MCP protocol identification
- Binary name is now 'codeprism' for clean user experience
- All usage now follows pattern: 'codeprism --mcp' for server mode

This completes the binary rename alignment across all project documentation
and configuration files.

Author: milliondreams

README.md

@@ -142,7 +142,7 @@ cd codeprism
 cargo build --release
 
 # Verify installation
-./target/release/codeprism-mcp-server --help
+./target/release/codeprism --help
 ```
 
 **⚠️ Development Note**: This project enforces strict implementation completeness standards via git pre-commit hooks. All commits must contain complete, functional implementations with zero placeholder code. The existing `.git/hooks/pre-commit` script automatically validates code quality and implementation completeness.
@@ -157,7 +157,8 @@ cargo build --release
 {
   "mcpServers": {
     "codeprism": {
-      "command": "/path/to/codeprism/target/release/codeprism-mcp-server",
+      "command": "/path/to/codeprism/target/release/codeprism",
+      "args": ["--mcp"],
       "env": {
         "CODEPRISM_PROFILE": "development",
         "RUST_LOG": "info"
@@ -173,7 +174,8 @@ cargo build --release
 {
   "mcpServers": {
     "codeprism": {
-      "command": "/path/to/codeprism/target/release/codeprism-mcp-server",
+      "command": "/path/to/codeprism/target/release/codeprism",
+      "args": ["--mcp"],
       "env": {
         "CODEPRISM_PROFILE": "development",
         "RUST_LOG": "info"
@@ -188,7 +190,7 @@ cargo build --release
 # Set configuration and run
 export CODEPRISM_PROFILE=development
 export RUST_LOG=info
-./target/release/codeprism-mcp-server
+./target/release/codeprism --mcp
 ```
 
 ## 🛠️ Available Tools
@@ -398,14 +400,14 @@ cargo install codeprism-mcp-server
 **Download Binary:**
 ```bash
 # Linux x86_64
-wget https://github.com/rustic-ai/codeprism/releases/latest/download/codeprism-mcp-server-linux-x86_64
-chmod +x codeprism-mcp-server-linux-x86_64
+wget https://github.com/rustic-ai/codeprism/releases/latest/download/codeprism-linux-x86_64
+chmod +x codeprism-linux-x86_64
 
 # macOS
-wget https://github.com/rustic-ai/codeprism/releases/latest/download/codeprism-mcp-server-macos-x86_64
+wget https://github.com/rustic-ai/codeprism/releases/latest/download/codeprism-macos-x86_64
 
 # Windows
-# Download from: https://github.com/rustic-ai/codeprism/releases/latest/download/codeprism-mcp-server-windows-x86_64.exe
+# Download from: https://github.com/rustic-ai/codeprism/releases/latest/download/codeprism-windows-x86_64.exe
 ```
 
 **Docker:**

codeprism-docs/docs/mcp-server/getting-started/large-repositories.md

@@ -21,7 +21,7 @@ This means for most repositories, you can simply run:
 ```bash
 export CODEPRISM_PROFILE=development
 export REPOSITORY_PATH=/path/to/your/repository
-./target/release/codeprism-mcp-server
+./target/release/codeprism --mcp
 ```
 
 ## Default Configuration
@@ -114,7 +114,7 @@ graph TD
 ```bash
 export CODEPRISM_PROFILE=development
 export REPOSITORY_PATH=/path/to/repo
-./target/release/codeprism-mcp-server
+./target/release/codeprism --mcp
 ```
 - **Excludes**: All dependency directories (`.tox`, `venv`, `node_modules`, etc.)
 - **Pros**: Fast indexing, low memory usage, focuses on your code
@@ -125,7 +125,7 @@ export REPOSITORY_PATH=/path/to/repo
 export CODEPRISM_PROFILE=development
 export CODEPRISM_DEPENDENCY_MODE=smart
 export REPOSITORY_PATH=/path/to/repo
-./target/release/codeprism-mcp-server
+./target/release/codeprism --mcp
 ```
 - **Includes**: Public APIs and commonly used dependency files only
 - **Excludes**: Internal implementation details, tests, documentation
@@ -138,7 +138,7 @@ export REPOSITORY_PATH=/path/to/repo
 export CODEPRISM_PROFILE=production
 export CODEPRISM_DEPENDENCY_MODE=include_all
 export REPOSITORY_PATH=/path/to/repo
-./target/release/codeprism-mcp-server
+./target/release/codeprism --mcp
 ```
 - **Includes**: Everything including full dependency source code
 - **Pros**: Complete code intelligence, full import following, comprehensive analysis
@@ -163,7 +163,7 @@ export CODEPRISM_PROFILE=development
 export CODEPRISM_MEMORY_LIMIT_MB=4096
 export CODEPRISM_DEPENDENCY_MODE=smart
 export REPOSITORY_PATH=/path/to/repo
-./target/release/codeprism-mcp-server
+./target/release/codeprism --mcp
 ```
 
 2. **Use complete analysis** when you need full dependency intelligence:
@@ -172,14 +172,14 @@ export CODEPRISM_PROFILE=production
 export CODEPRISM_MEMORY_LIMIT_MB=8192
 export CODEPRISM_DEPENDENCY_MODE=include_all
 export REPOSITORY_PATH=/path/to/repo
-./target/release/codeprism-mcp-server
+./target/release/codeprism --mcp
 ```
 
 3. **Use minimal mode** for CI/CD or when performance is critical:
 ```bash
 export CODEPRISM_PROFILE=development
 export REPOSITORY_PATH=/path/to/repo
-./target/release/codeprism-mcp-server  # Default
+./target/release/codeprism --mcp  # Default
 ```
 
 ### Very Large Repositories (>50,000 files)
@@ -188,7 +188,7 @@ export CODEPRISM_PROFILE=enterprise
 export CODEPRISM_MEMORY_LIMIT_MB=8192
 export CODEPRISM_BATCH_SIZE=20
 export REPOSITORY_PATH=/path/to/huge/repo
-./target/release/codeprism-mcp-server
+./target/release/codeprism --mcp
 ```
 
 ### Specific Language Focus
@@ -197,13 +197,13 @@ export REPOSITORY_PATH=/path/to/huge/repo
 export CODEPRISM_PROFILE=development
 export CODEPRISM_INCLUDE_EXTENSIONS="py,js,ts"
 export REPOSITORY_PATH=/path/to/repo
-./target/release/codeprism-mcp-server
+./target/release/codeprism --mcp
 
 # Only Rust projects  
 export CODEPRISM_PROFILE=development
 export CODEPRISM_INCLUDE_EXTENSIONS="rs,toml"
 export REPOSITORY_PATH=/path/to/repo
-./target/release/codeprism-mcp-server
+./target/release/codeprism --mcp
 ```
 
 ### Memory-Constrained Systems
@@ -213,7 +213,7 @@ export CODEPRISM_PROFILE=development
 export CODEPRISM_MEMORY_LIMIT_MB=2048
 export CODEPRISM_BATCH_SIZE=15
 export REPOSITORY_PATH=/path/to/repo
-./target/release/codeprism-mcp-server
+./target/release/codeprism --mcp
 ```
 
 ### Include All File Types
@@ -222,7 +222,7 @@ export REPOSITORY_PATH=/path/to/repo
 export CODEPRISM_PROFILE=development
 export CODEPRISM_INCLUDE_EXTENSIONS="*"
 export REPOSITORY_PATH=/path/to/repo
-./target/release/codeprism-mcp-server
+./target/release/codeprism --mcp
 ```
 
 ## Environment Variables Reference
@@ -260,7 +260,7 @@ export CODEPRISM_PROFILE=development
 export CODEPRISM_MEMORY_LIMIT_MB=1024
 export CODEPRISM_INCLUDE_EXTENSIONS="*"
 export REPOSITORY_PATH=/path/to/repo
-./target/release/codeprism-mcp-server
+./target/release/codeprism --mcp
 ```
 
 ## Examples
@@ -270,7 +270,7 @@ export REPOSITORY_PATH=/path/to/repo
 # Uses optimized defaults - works for most repositories
 export CODEPRISM_PROFILE=development
 export REPOSITORY_PATH=/path/to/your/repository
-./target/release/codeprism-mcp-server
+./target/release/codeprism --mcp
 ```
 
 ### Custom Configuration Examples
@@ -280,19 +280,19 @@ export CODEPRISM_PROFILE=development
 export CODEPRISM_MEMORY_LIMIT_MB=1024
 export CODEPRISM_BATCH_SIZE=15
 export REPOSITORY_PATH=/path/to/repo
-./target/release/codeprism-mcp-server
+./target/release/codeprism --mcp
 
 # Maximum performance (if you have lots of RAM)
 export CODEPRISM_PROFILE=enterprise
 export CODEPRISM_MEMORY_LIMIT_MB=16384
 export CODEPRISM_BATCH_SIZE=50
 export REPOSITORY_PATH=/path/to/repo
-./target/release/codeprism-mcp-server
+./target/release/codeprism --mcp
 
 # Use production profile for complete analysis
 export CODEPRISM_PROFILE=production
 export REPOSITORY_PATH=/path/to/repo
-./target/release/codeprism-mcp-server
+./target/release/codeprism --mcp
 ```
 
 The new defaults should handle most real-world repositories without any configuration needed! 

codeprism-docs/docs/mcp-server/tools-documentation.md

@@ -450,15 +450,16 @@ export CODEPRISM_PROFILE=development
 export REPOSITORY_PATH=/path/to/your/repository
 
 # Start CodePrism MCP server
-./target/release/codeprism-mcp-server
+./target/release/codeprism --mcp
 ```
 
 #### Client Configuration (Claude Desktop)
 ```json
 {
   "mcpServers": {
     "codeprism": {
-      "command": "./target/release/codeprism-mcp-server",
+      "command": "./target/release/codeprism",
+      "args": ["--mcp"],
       "env": {
         "CODEPRISM_PROFILE": "development",
         "REPOSITORY_PATH": "/path/to/repository"

codeprism-docs/docs/parsers/rust-implementation.md

@@ -420,7 +420,7 @@ The Rust parser will automatically be available through the MCP server for:
 ### CLI Integration
 ```bash
 # Analyze codeprism itself
-export REPOSITORY_PATH=/path/to/codeprism && ./target/release/codeprism-mcp-server
+export REPOSITORY_PATH=/path/to/codeprism && ./target/release/codeprism --mcp
 
 # Focus on Rust files only
 prism analyze --language rust /path/to /codeprism

crates/codeprism-moth-specs/codeprism/tools/codeprism-javascript-analysis.yaml

@@ -17,7 +17,7 @@ capabilities:
 # Server startup configuration  
 server:
   command: "cargo"
-  args: ["run", "--package", "codeprism-mcp-server", "--bin", "codeprism-mcp-server"]
+  args: ["run", "--package", "codeprism-mcp-server", "--bin", "codeprism", "--", "--mcp"]
   env:
     RUST_LOG: "info"
     MCP_PROTOCOL_VERSION: "2025-06-18"

docs/PRISM-MCP-SERVER-DESCRIPTION.md

@@ -567,7 +567,8 @@ CodeCodePrism is designed to work seamlessly with major MCP clients:
 {
   "mcpServers": {
     "codeprism": {
-      "command": "codeprism-mcp-server",
+              "command": "codeprism",
+        "args": ["--mcp"],
       "env": {
         "CODEPRISM_PROFILE": "development",
         "RUST_LOG": "info"
@@ -582,7 +583,8 @@ CodeCodePrism is designed to work seamlessly with major MCP clients:
 {
   "mcpServers": {
     "codeprism": {
-      "command": "codeprism-mcp-server",
+              "command": "codeprism",
+        "args": ["--mcp"],
       "env": {
         "CODEPRISM_PROFILE": "development",
         "RUST_LOG": "info"
@@ -613,7 +615,7 @@ CodeCodePrism is designed to work seamlessly with major MCP clients:
 # Set configuration and start CodePrism MCP server
 export CODEPRISM_PROFILE=development
 export RUST_LOG=info
-codeprism-mcp-server
+codeprism --mcp
 
 # The MCP server is designed to be launched by MCP clients
 # Not as a standalone command-line tool

docs/RUST_PARSER_IMPLEMENTATION.md

@@ -414,7 +414,7 @@ The Rust parser will automatically be available through the MCP server for:
 ### CLI Integration
 ```bash
 # Analyze codeprism itself
-export REPOSITORY_PATH=/path/to/codeprism && ./target/release/codeprism-mcp-server
+export REPOSITORY_PATH=/path/to/codeprism && ./target/release/codeprism --mcp
 
 # Focus on Rust files only
 prism analyze --language rust /path/to /codeprism

test-harness-fixed.yaml

@@ -18,7 +18,7 @@ global:
 
 server:
   start_command: "cargo"
-  args: ["run", "--bin", "codeprism-mcp-server", "--"]
+      args: ["run", "--bin", "codeprism", "--", "--mcp"]
   env: {}
   working_dir: "."
   startup_timeout_seconds: 30

test-harness.yaml

@@ -19,7 +19,7 @@ global:
     json_format: false
 
 server:
-  start_command: "cargo run --bin codeprism-mcp-server"
+      start_command: "cargo run --bin codeprism -- --mcp"
   args:
     - "stdio"
   env: {}

tests/mcp_tools/comprehensive_mcp_tests.rs

@@ -113,7 +113,7 @@ impl McpServerClient {
         println!("🚀 Starting MCP server for end-to-end testing...");
 
         let mut cmd = Command::new("cargo");
-        cmd.args(&["run", "--bin", "codeprism-mcp-server", "--", "stdio"])
+        cmd.args(&["run", "--bin", "codeprism", "--", "--mcp", "stdio"])
             .kill_on_drop(true);
 
         let child = cmd.spawn()?;