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.

.claude/workflows/file-modification.md

@@ -1,29 +1,48 @@
-## File Modification
+# File Modification
 
-### Use edit_file (MCP)
-- Built-in Edit tool failed 1+ times
-- Need dry-run preview before applying changes
-- Need line-based operations (insert_after, insert_before)
-- Need to replace all occurrences at once
-- Built-in Edit returns "old_string not found"
-- Whitespace/formatting issues in built-in Edit
+Before modifying files, always:
+- Try built-in Edit tool first
+- Escalate to MCP tools when built-ins fail
+- Use write_file only as last resort
 
-**Mode Selection**:
-- `mode=update`: Replace text
-- `mode=line`: Line-based operations
+## MCP Tools Usage
 
-### Use write_file (MCP)
-- Creating brand new files
-- MCP edit_file still fails (last resort)
-- Need to completely replace file content
-- Need backup before overwriting
-- User explicitly asks to "recreate file"
+### edit_file - Modify Files
+
+**When**: Built-in Edit fails, need dry-run preview, or need line-based operations
+
+**How**:
+```javascript
+edit_file(path="/file.ts", oldText="old", newText="new")              // Replace text
+edit_file(path="/file.ts", oldText="old", newText="new", dryRun=true) // Preview diff
+edit_file(path="/file.ts", oldText="old", newText="new", replaceAll=true) // Replace all
+edit_file(path="/file.ts", mode="line", operation="insert_after", line=10, text="new line")
+edit_file(path="/file.ts", mode="line", operation="delete", line=5, end_line=8)
+```
+
+**Modes**: `update` (replace text, default), `line` (line-based operations)
+
+**Operations** (line mode): `insert_before`, `insert_after`, `replace`, `delete`
+
+---
+
+### write_file - Create/Overwrite Files
+
+**When**: Create new files, completely replace content, or edit_file still fails
+
+**How**:
+```javascript
+write_file(path="/new-file.ts", content="file content here")
+write_file(path="/existing.ts", content="...", backup=true)  // Create backup first
+```
+
+---
 
 ## Priority Logic
 
 **File Reading**:
 1. Known single file → Built-in Read
-2. Multiple files OR pattern matching → read_file (MCP)
+2. Multiple files OR pattern matching → smart_search (MCP)
 3. Unknown location → smart_search then Read
 4. Large codebase + repeated access → smart_search (indexed)
 
@@ -33,9 +52,9 @@
 3. Still fails → write_file (MCP)
 
 **Search**:
-1. External knowledge → Exa
+1. External knowledge → Exa (MCP)
 2. Exact pattern in small codebase → Built-in Grep
-3. Semantic/unknown location → smart_search
+3. Semantic/unknown location → smart_search (MCP)
 4. Large codebase + repeated searches → smart_search (indexed)
 
 ## Decision Triggers
@@ -45,4 +64,3 @@
 **Use semantic search** for exploratory tasks
 **Use indexed search** for large, stable codebases
 **Use Exa** for external/public knowledge
-