Address PR #27 review feedback: path normalization, tests, and conventions

[Copilot]

📝 Update Information

Primitive Details

• Type: Both (Tools and Supporting Infrastructure)
• Name: Multiple utilities and tools using path resolution
• Update Category: Bug Fix, Code Quality, Test Coverage

⚠️ CRITICAL: PR SCOPE VALIDATION

This PR is for updating existing MCP server primitives and must ONLY include these file types:

✅ ALLOWED FILES:

• Server implementation files (server/src/**/*.ts)
• Updated primitive implementations
• Modified registration files (server/src/tools/*.ts)
• Updated or new test files (server/test/**/*.ts)
• Documentation updates (README.md, server docs)
• Updated type definitions (server/src/types/*.ts)
• Modified supporting library files (server/src/lib/*.ts)
• Configuration updates if needed (package.json, tsconfig.json)

🚫 FORBIDDEN FILES:

• Files unrelated to the primitive update
• Temporary or test output files
• IDE configuration files
• Log files or debug output
• Analysis or summary files

Rationale: This PR should contain only the files necessary to update and test the primitive.

🚨 PRs that include forbidden files will be rejected and must be revised.

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🛑 MANDATORY PR VALIDATION CHECKLIST

BEFORE SUBMITTING THIS PR, CONFIRM:

• ONLY server implementation files are included
• NO temporary or output files are included
• NO unrelated configuration files are included
• ALL existing tests continue to pass
• NEW functionality is properly tested

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• Impact Scope: Localized (path resolution utilities and related tests)

Update Metadata

• Breaking Changes: No
• API Compatibility: Maintained
• Performance Impact: Neutral (normalization adds negligible overhead)

🎯 Changes Description

Current Behavior

Review feedback identified several issues:

1. Import ordering violated alphabetical convention in language-server.ts
2. Monitoring storage directory lost leading dot, breaking .gitignore patterns
3. CODEQL_MCP_TMP_DIR accepted relative paths without normalization, causing unpredictable resolution
4. Missing unit tests for getPackageVersion() and getUserWorkspaceDir()
5. Missing test coverage for relative path resolution in CLI tools

Updated Behavior

• Imports alphabetically ordered within categories
• Monitoring storage restored to .ql-mcp-tracking (hidden, matches .gitignore)
• CODEQL_MCP_TMP_DIR relative paths now normalized against process.cwd()
• Comprehensive unit tests for version and workspace utilities
• Test coverage for relative path resolution in tests, database, dir/packDir parameters

Motivation

Addresses all PR #27 review feedback to ensure code quality, correctness, and maintainability.

🔄 Before vs. After Comparison

Path Normalization

// BEFORE: Relative paths used as-is
const PROJECT_TMP_BASE = process.env.CODEQL_MCP_TMP_DIR || join(getPackageRootDir(), '.tmp');

// AFTER: Relative paths normalized against cwd
const PROJECT_TMP_BASE = process.env.CODEQL_MCP_TMP_DIR
  ? (isAbsolute(process.env.CODEQL_MCP_TMP_DIR) 
      ? process.env.CODEQL_MCP_TMP_DIR 
      : resolve(process.cwd(), process.env.CODEQL_MCP_TMP_DIR))
  : join(getPackageRootDir(), '.tmp');

Storage Location

// BEFORE: Missing leading dot
storageLocation: process.env.MONITORING_STORAGE_LOCATION || join(getProjectTmpBase(), 'ql-mcp-tracking')

// AFTER: Restored leading dot to match .gitignore
storageLocation: process.env.MONITORING_STORAGE_LOCATION || join(getProjectTmpBase(), '.ql-mcp-tracking')

Import Ordering

// BEFORE: Out of alphabetical order
import { getProjectTmpDir } from '../utils/temp-dir';
import { getResolvedCodeQLDir } from './cli-executor';
import { getPackageVersion } from '../utils/package-paths';

// AFTER: Alphabetically ordered within relative imports
import { getPackageVersion } from '../utils/package-paths';
import { getProjectTmpDir } from '../utils/temp-dir';
import { getResolvedCodeQLDir } from './cli-executor';

🧪 Testing & Validation

Test Coverage Updates

• Existing Tests: All 384 unit tests pass
• New Test Cases: Added 6 new test cases
• Regression Tests: Covers path resolution edge cases
• Edge Case Tests: Relative vs absolute path handling

Validation Scenarios

1. Path Normalization: Tests verify CODEQL_MCP_TMP_DIR with relative paths resolves correctly
2. Version Caching: Tests confirm getPackageVersion() reads package.json once and caches result
3. Workspace Resolution: Tests validate env override and monorepo vs npm-installed fallback behavior
4. Relative Path Resolution: Tests ensure CLI tools resolve relative tests, database, dir/packDir against user workspace

Test Results

• Unit Tests: All pass (384/384 tests, +6 new)
• Integration Tests: All pass except pre-existing network failure (45/46)
• Manual Testing: Validated path resolution behavior
• Performance Testing: No regressions detected

📋 Implementation Details

Files Modified

• Core Implementation: server/src/utils/temp-dir.ts, server/src/utils/package-paths.ts
• Supporting Libraries: server/src/lib/language-server.ts, server/src/lib/session-data-manager.ts
• Tests: server/test/src/utils/package-paths.test.ts, server/test/src/lib/cli-tool-registry.test.ts
• Documentation: Comments updated for clarity

Code Changes Summary

• Error Handling: Path normalization prevents relative-path bugs
• Type Safety: Maintained existing TypeScript types
• Input Validation: Added isAbsolute() check for env var paths
• Output Format: No changes to output formats

Dependencies

• No New Dependencies: Uses existing path module functions

🔍 Quality Improvements

Bug Fixes

• Issue: Relative paths in CODEQL_MCP_TMP_DIR could resolve unpredictably
• Root Cause: No normalization of env var before use
• Solution: Check isAbsolute() and resolve() against process.cwd()
• Prevention: Added comment documenting normalization requirement

Code Quality Enhancements

• Readability: Clearer comments on path resolution logic
• Maintainability: Import ordering matches project conventions
• Testability: New tests prevent regressions
• Reusability: Path normalization pattern documented for reuse

🔗 References

Related Issues/PRs

• Related PRs: PR Use dynamic package version and respect CODEQL_MCP_TMP_DIR env var #27 (original changes), PR More prep for initial public release readiness #24 (feedback source)

Validation Materials

• Test Cases: 6 new unit tests covering path resolution and utility functions
• Performance Benchmarks: No measurable impact on test execution time

🚀 Compatibility & Migration

Backward Compatibility

• Fully Compatible: No breaking changes
• Deprecation Warnings: None
• Breaking Changes: None

API Evolution

• Enhanced Parameters: None
• Improved Responses: None
• Better Error Messages: Path resolution more predictable
• Maintained Contracts: All API contracts preserved

👥 Review Guidelines

For Reviewers

Please verify:

• ⚠️ SCOPE COMPLIANCE: PR contains only server implementation files
• ⚠️ NO UNRELATED FILES: No temporary, output, or unrelated files
• ⚠️ BACKWARD COMPATIBILITY: Existing functionality preserved
• Functionality: Updates work as described
• Test Coverage: All existing tests pass, new tests comprehensive
• Performance: No performance regressions
• Code Quality: Maintains or improves code quality
• Documentation: Updated documentation accurate
• Error Handling: Improved error handling
• Type Safety: TypeScript types properly updated

Testing Instructions

# Full test suite
npm install
npm run build-and-test

# Server unit tests only
npm run test:server

# Code quality checks
npm run lint
npm run format:check

Validation Checklist

1. Regression Testing: All 384 unit tests pass
2. New Feature Testing: 6 new tests validate path normalization and utilities
3. Performance Testing: No measurable performance impact
4. Error Testing: Path edge cases covered
5. Integration Testing: Integration tests pass (1 pre-existing network failure unrelated)
6. Documentation Review: Comments accurate and helpful

📊 Impact Assessment

Performance Impact

• Memory Usage: No change (minimal additional logic)
• Execution Time: Negligible (single isAbsolute() and resolve() call at module init)
• Throughput: No impact

Server Impact

• Startup Time: No measurable impact
• Runtime Stability: Improved (eliminates relative path ambiguity)
• Resource Usage: No change
• Concurrent Usage: Safe (module-level constant initialized once)

AI Assistant Impact

• Enhanced Accuracy: More predictable path resolution
• Better Coverage: Test coverage expanded
• Improved Reliability: Eliminates edge case bugs
• Enhanced User Experience: Hidden tracking files reduce noise

🔄 Deployment Strategy

Rollout Considerations

• Safe Deployment: Safe for immediate deployment
• Gradual Rollout: Not required (low-risk changes)
• Monitoring: Standard monitoring sufficient
• Rollback Plan: Simple revert if needed

Post-Deployment Validation

• Monitoring: Monitor for path resolution errors (expect none)
• User Feedback: No user-visible changes
• Performance Tracking: CPU/memory usage unchanged
• Error Tracking: Watch for CODEQL_MCP_TMP_DIR-related errors (expect reduction)

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Update Methodology: This update follows best practices:

1. ✅ Comprehensive backward compatibility analysis
2. ✅ Thorough testing of all changes
3. ✅ Performance impact assessment
4. ✅ Clear documentation of changes
5. ✅ Robust error handling improvements
6. ✅ Maintained code quality standards

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