fix: Resolve MCP installation issues and enhance path resolution

- Fixed API endpoint mismatches in mcp-manager.js to ensure global install/update buttons function correctly.
- Corrected undefined function references in mcp-manager.js for project installation.
- Refactored event handling to eliminate global scope pollution in mcp-manager.js.
- Added comprehensive debugging guide for MCP installation issues.
- Implemented a session path resolver to infer content types from filenames and paths, improving usability.
- Introduced tests for embeddings improvements in init and status commands to verify functionality.

EMBEDDINGS_IMPROVEMENTS_SUMMARY.md

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+# CodexLens Embeddings Statistics Improvements
+
+## Summary
+
+Improved the CodexLens `init` and `status` commands to return comprehensive embeddings statistics, making it easy for users to understand embeddings coverage.
+
+## Changes Made
+
+### 1. Updated `init` command (Task 1)
+
+**File**: `codex-lens/src/codexlens/cli/commands.py` (lines 142-219)
+
+**Key Changes**:
+- Changed from `generate_embeddings()` to `generate_embeddings_recursive()`
+- Now processes all `_index.db` files recursively in the index tree
+- Passes `index_root` (directory) instead of `index_path` (file)
+- Returns comprehensive coverage statistics after generation
+
+**Imports Added**:
+```python
+from codexlens.cli.embedding_manager import generate_embeddings_recursive, get_embeddings_status
+```
+
+**Result Structure**:
+```json
+{
+  "embeddings": {
+    "generated": true,
+    "total_indexes": 26,
+    "total_files": 303,
+    "files_with_embeddings": 303,
+    "coverage_percent": 100.0,
+    "total_chunks": 500
+  }
+}
+```
+
+**Console Output**:
+- Shows files processed count
+- Shows total chunks created
+- Shows indexes processed (successful/total)
+
+### 2. Updated `status` command (Task 2)
+
+**File**: `codex-lens/src/codexlens/cli/commands.py` (lines 642-713)
+
+**Key Changes**:
+- Added embeddings coverage check using `get_embeddings_status()`
+- Updates `vector_search` feature flag based on coverage (>= 50%)
+- Includes embeddings data in JSON output
+- Displays embeddings statistics in console output
+
+**Imports Added**:
+```python
+from codexlens.cli.embedding_manager import get_embeddings_status
+```
+
+**Result Structure**:
+```json
+{
+  "embeddings": {
+    "total_indexes": 26,
+    "total_files": 303,
+    "files_with_embeddings": 303,
+    "files_without_embeddings": 0,
+    "coverage_percent": 100.0,
+    "total_chunks": 500,
+    "indexes_with_embeddings": 26,
+    "indexes_without_embeddings": 0
+  },
+  "features": {
+    "exact_fts": true,
+    "fuzzy_fts": true,
+    "hybrid_search": true,
+    "vector_search": true  // true when coverage >= 50%
+  }
+}
+```
+
+**Console Output**:
+```
+Search Backends:
+  Exact FTS: ✓ (unicode61)
+  Fuzzy FTS: ✓ (trigram)
+  Hybrid Search: ✓ (RRF fusion)
+  Vector Search: ✓ (embeddings available)
+
+Embeddings Coverage:
+  Total Indexes: 26
+  Total Files: 303
+  Files with Embeddings: 303
+  Coverage: 100.0%
+  Total Chunks: 500
+```
+
+## Benefits
+
+1. **Transparency**: Users can now see exactly what embeddings were generated
+2. **Coverage Visibility**: Clear percentage showing embeddings coverage across all files
+3. **Recursive Processing**: All index databases in the tree are processed, not just the root
+4. **Feature Detection**: Vector search is automatically enabled when coverage is sufficient (>= 50%)
+5. **Comprehensive Stats**: Shows total indexes, files, chunks, and coverage percentage
+
+## Backward Compatibility
+
+- All changes are backward compatible
+- Gracefully handles cases where embeddings are not available
+- ImportError handling for when embedding_manager is not available
+- Existing JSON output structure is extended, not changed
+
+## Testing
+
+Created test script: `test_embeddings_improvements.py`
+
+Tests verify:
+- Init command reports embeddings statistics correctly
+- Status command shows embeddings coverage
+- JSON output includes all required fields
+- Console output displays statistics properly
+
+## Usage Examples
+
+### Init with embeddings
+```bash
+codexlens init /path/to/project --json
+# Returns comprehensive embeddings statistics
+```
+
+### Check status
+```bash
+codexlens status --json
+# Shows embeddings coverage and feature availability
+```
+
+### Init without embeddings
+```bash
+codexlens init /path/to/project --no-embeddings --json
+# Returns embeddings: {"generated": false, "error": "Skipped (--no-embeddings)"}
+```
+
+## Files Modified
+
+1. `codex-lens/src/codexlens/cli/commands.py` - Updated init and status commands
+
+## Implementation Details
+
+### Init Command Flow
+1. Build index tree as before
+2. If `--no-embeddings` not set:
+   - Call `generate_embeddings_recursive(index_root)` instead of `generate_embeddings(index_path)`
+   - After generation, call `get_embeddings_status(index_root)` to get coverage stats
+   - Include comprehensive statistics in result
+3. Return result with embeddings coverage data
+
+### Status Command Flow
+1. Collect index statistics as before
+2. Call `get_embeddings_status(index_root)` to check embeddings
+3. Set `vector_search` feature flag based on coverage >= 50%
+4. Include embeddings info in JSON output
+5. Display embeddings statistics in console output
+
+## Error Handling
+
+- Handles ImportError when embedding_manager not available
+- Handles cases where embeddings don't exist (returns 0% coverage)
+- Graceful fallback if get_embeddings_status fails
+- Debug logging for failed operations