deps(deps): bump rust from 1.80-slim to 1.93-slim

.claude/commands/update_docs.md

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+# Documentation Update Command for Code Intelligence MCP Server
+
+## Purpose
+Automate documentation updates after code changes, ensuring comprehensive and accurate documentation for the Code Intelligence MCP Server project.
+
+## 🔍 Documentation Update Strategy
+
+### 1. Automated Documentation Analysis
+
+Use the specialized agent for enterprise-level documentation updates:
+
+```bash
+# Use documentation architect for comprehensive doc updates
+Task(
+  description="Update Code Intelligence docs",
+  prompt="Review and update all project documentation after recent changes, ensure enterprise-level standards for MCP server documentation, fix broken references, maintain coherent structure for TypeScript/Rust hybrid architecture",
+  subagent_type="general-purpose"
+)
+```
+
+The agent will:
+- Update README.md with latest features and API changes
+- Fix broken references in specs/ directory
+- Ensure docs/ structure is coherent
+- Update MCP protocol documentation
+- Maintain architecture diagrams accuracy
+- Update API documentation
+
+### 2. Enhanced Documentation Analysis (with MCP-REPL)
+
+**🚀 Semantic Documentation Discovery:**
+
+```bash
+# Find documentation patterns in TypeScript MCP
+mcp__mcp-repl__searchcode(
+  query="MCP protocol documentation tools resources API",
+  workingDirectory="F:/Development/Projects/ProjectAra/typescript-mcp"
+)
+
+# Find documentation patterns in Rust core
+mcp__mcp-repl__searchcode(
+  query="documentation examples /// doc comments",
+  workingDirectory="F:/Development/Projects/ProjectAra/rust-core"
+)
+```
+
+**🔍 Code-Documentation Consistency Check:**
+
+```bash
+# Verify TypeScript MCP examples work correctly
+mcp__mcp-repl__executenodejs(
+  code=`
+    const fs = require('fs');
+    const path = require('path');
+
+    // Read and validate MCP tool examples from docs
+    const docsPath = path.join(process.cwd(), 'specs/001-code-ntelligence-mcp');
+    const contractsPath = path.join(process.cwd(), 'typescript-mcp/tests/contract');
+
+    // Validate that documented tools match contract tests
+    const contractTests = [
+      'test_search_code.ts',
+      'test_explain_function.ts',
+      'test_find_references.ts',
+      'test_trace_data_flow.ts',
+      'test_analyze_security.ts',
+      'test_get_api_endpoints.ts',
+      'test_check_complexity.ts'
+    ];
+
+    contractTests.forEach(test => {
+      const testPath = path.join(contractsPath, test);
+      if (fs.existsSync(testPath)) {
+        console.log('✅ Contract test exists:', test);
+      } else {
+        console.error('❌ Missing contract test:', test);
+      }
+    });
+  `,
+  workingDirectory="F:/Development/Projects/ProjectAra"
+)
+```
+
+**📊 Structural Documentation Analysis:**
+
+```bash
+# Analyze documentation structure for MCP tools
+mcp__mcp-repl__astgrep_enhanced_search(
+  pattern="export function $TOOL_NAME($$$ARGS) { $$$ }",
+  workingDirectory="F:/Development/Projects/ProjectAra/typescript-mcp",
+  includeMetadata=true
+)
+
+# Find Rust documentation patterns
+mcp__mcp-repl__astgrep_enhanced_search(
+  pattern="/// $DOC_COMMENT\npub fn $FUNC_NAME($$$ARGS) { $$$ }",
+  workingDirectory="F:/Development/Projects/ProjectAra/rust-core",
+  language="rust"
+)
+```
+
+### 3. Documentation Validation Checklist
+
+**Core Documentation Files:**
+- [ ] README.md - Main project documentation
+- [ ] CLAUDE.md - Claude Code specific instructions
+- [ ] specs/001-code-ntelligence-mcp/spec.md - Feature specification
+- [ ] specs/001-code-ntelligence-mcp/quickstart.md - Quick start guide
+- [ ] typescript-mcp/README.md - TypeScript MCP documentation
+- [ ] rust-core/README.md - Rust core documentation
+
+**API Documentation:**
+- [ ] MCP Protocol tools documentation
+- [ ] REST API endpoints (port 4000)
+- [ ] WebSocket endpoints (port 8080)
+- [ ] FFI bridge documentation
+
+**Architecture Documentation:**
+- [ ] System architecture diagram
+- [ ] Data flow diagrams
+- [ ] Component interaction diagrams
+- [ ] Database schema documentation
+
+### 4. Automated Documentation Generation
+
+**Generate TypeScript API Documentation:**
+```bash
+cd typescript-mcp
+npx typedoc --out ../docs/api/typescript src/
+```
+
+**Generate Rust Documentation:**
+```bash
+cd rust-core
+cargo doc --no-deps --document-private-items
+cp -r target/doc ../docs/api/rust
+```
+
+**Generate MCP Tools Documentation:**
+```bash
+mcp__mcp-repl__executenodejs(
+  code=`
+    const fs = require('fs');
+    const path = require('path');
+
+    // Extract MCP tools from contract tests
+    const contractsPath = 'typescript-mcp/tests/contract';
+    const tools = [];
+
+    const files = fs.readdirSync(contractsPath);
+    files.forEach(file => {
+      if (file.startsWith('test_') && file.endsWith('.ts')) {
+        const toolName = file.replace('test_', '').replace('.ts', '');
+        tools.push({
+          name: toolName,
+          file: file,
+          description: getToolDescription(toolName)
+        });
+      }
+    });
+
+    // Generate markdown documentation
+    let markdown = '# MCP Tools Documentation\\n\\n';
+    tools.forEach(tool => {
+      markdown += \`## \${tool.name}\\n\\n\`;
+      markdown += \`\${tool.description}\\n\\n\`;
+      markdown += \`Contract Test: \\\`\${tool.file}\\\`\\n\\n\`;
+    });
+
+    fs.writeFileSync('docs/mcp-tools.md', markdown);
+    console.log('✅ Generated MCP tools documentation');
+
+    function getToolDescription(name) {
+      const descriptions = {
+        'search_code': 'Natural language code search across the codebase',
+        'explain_function': 'Explain what a specific function does',
+        'find_references': 'Find all references to a symbol',
+        'trace_data_flow': 'Trace data flow through the code',
+        'analyze_security': 'Analyze code for security vulnerabilities',
+        'get_api_endpoints': 'List all API endpoints in the codebase',
+        'check_complexity': 'Analyze code complexity metrics'
+      };
+      return descriptions[name] || 'Tool description pending';
+    }
+  `,
+  workingDirectory="F:/Development/Projects/ProjectAra"
+)
+```
+
+### 5. Documentation Linting and Validation
+
+**Lint Markdown Files:**
+```bash
+npx markdownlint "**/*.md" --fix
+```
+
+**Check for Broken Links:**
+```bash
+npx markdown-link-check README.md
+npx markdown-link-check specs/**/*.md
+```
+
+**Validate Code Examples:**
+```bash
+# Extract and test code examples from markdown
+mcp__mcp-repl__executenodejs(
+  code=`
+    const fs = require('fs');
+    const path = require('path');
+
+    function extractCodeBlocks(markdown) {
+      const codeBlockRegex = /\\\`\\\`\\\`(javascript|typescript|js|ts)\\n([\\s\\S]*?)\\n\\\`\\\`\\\`/g;
+      const blocks = [];
+      let match;
+      while ((match = codeBlockRegex.exec(markdown)) !== null) {
+        blocks.push({
+          language: match[1],
+          code: match[2]
+        });
+      }
+      return blocks;
+    }
+
+    // Test README.md examples
+    const readme = fs.readFileSync('README.md', 'utf8');
+    const codeBlocks = extractCodeBlocks(readme);
+
+    console.log(\`Found \${codeBlocks.length} code blocks in README.md\`);
+
+    codeBlocks.forEach((block, index) => {
+      try {
+        // Basic syntax check
+        if (block.language === 'javascript' || block.language === 'js') {
+          new Function(block.code);
+          console.log(\`✅ Code block \${index + 1} is valid\`);
+        }
+      } catch (error) {
+        console.error(\`❌ Code block \${index + 1} has syntax error:\`, error.message);
+      }
+    });
+  `,
+  workingDirectory="F:/Development/Projects/ProjectAra"
+)
+```
+
+### 6. Performance Documentation Update
+
+**Update Performance Benchmarks:**
+```bash
+# Run and document Rust benchmarks
+cd rust-core
+cargo bench > ../docs/performance/rust-benchmarks.txt
+
+# Run and document TypeScript performance
+cd ../typescript-mcp
+npm run test:performance > ../docs/performance/typescript-benchmarks.txt
+```
+
+### 7. Version and Changelog Management
+
+**Update Version Documentation:**
+```bash
+mcp__mcp-repl__executenodejs(
+  code=`
+    const fs = require('fs');
+    const pkg = JSON.parse(fs.readFileSync('package.json', 'utf8'));
+    const tsPkg = JSON.parse(fs.readFileSync('typescript-mcp/package.json', 'utf8'));
+
+    console.log('Current versions:');
+    console.log('Main package:', pkg.version);
+    console.log('TypeScript MCP:', tsPkg.version);
+
+    // Update CHANGELOG.md with version info
+    const date = new Date().toISOString().split('T')[0];
+    const changelog = fs.readFileSync('CHANGELOG.md', 'utf8');
+
+    if (!changelog.includes(pkg.version)) {
+      const newEntry = \`## [\${pkg.version}] - \${date}\\n\\n### Added\\n- [Add changes here]\\n\\n\`;
+      const updatedChangelog = changelog.replace('# Changelog\\n\\n', \`# Changelog\\n\\n\${newEntry}\`);
+      fs.writeFileSync('CHANGELOG.md', updatedChangelog);
+      console.log('✅ Updated CHANGELOG.md');
+    }
+  `,
+  workingDirectory="F:/Development/Projects/ProjectAra"
+)
+```
+
+## 📋 Documentation Update Workflow
+
+1. **Pre-Update Analysis:**
+   - Run semantic search to find outdated docs
+   - Check for broken links and references
+   - Identify missing documentation
+
+2. **Update Documentation:**
+   - Update API documentation
+   - Update architecture diagrams
+   - Fix code examples
+   - Update configuration examples
+
+3. **Validation:**
+   - Lint all markdown files
+   - Test code examples
+   - Verify links work
+   - Check cross-references
+
+4. **Generate Documentation:**
+   - Generate API docs from code
+   - Create MCP tools reference
+   - Update performance benchmarks
+
+5. **Final Review:**
+   - Ensure CLAUDE.md is up to date
+   - Verify README completeness
+   - Check specs alignment with implementation
+
+## 🎯 Quick Commands
+
+```bash
+# Full documentation update
+npm run docs:update
+
+# Generate API documentation
+npm run docs:generate
+
+# Validate documentation
+npm run docs:validate
+
+# Fix documentation issues
+npm run docs:fix
+```
+
+## 📝 Notes
+
+- Always update CLAUDE.md when adding new development practices
+- Keep README.md as the main entry point
+- Maintain specs/ directory for detailed technical documentation
+- Use docs/ directory for generated documentation
+- Follow Markdown best practices and linting rules
+- Ensure all code examples are tested and working