[BUG] Issue with indexing. It shows successful but index is not available after reindex.

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

The Issue

The claude-context MCP server has a bug where:

• Indexing appears to complete successfully (reports 191 files, 3334 chunks)
• But the index data doesn't persist or isn't accessible to search queries
• The status check and search queries are out of sync

What Should Happen?

index should be available after reindexing for queries

Error Messages/Logs

● Let me check the current indexing status to see what happened:

● claude-context - get_indexing_status (MCP)(path: "/home/mjh/code/TeamRPG-App/rpg-skills-matrix/web")
  ⎿  ✅ Codebase '/home/mjh/code/TeamRPG-App/rpg-skills-matrix/web' is fully indexed and ready for search.                                                                                                                                              
     📊 Statistics: 191 files, 3334 chunks
     📅 Status: completed
     🕐 Last updated: 10/23/2025, 8:27:07 PM

● Good news - it's now fully indexed! Let me try the semantic search again:

● claude-context - search_code (MCP)(path: "/home/mjh/code/TeamRPG-App/rpg-skills-matrix/web", query: "Project matching algorithm implementation scoring employees to projects", limit: 10)
  ⎿  Error: Codebase '/home/mjh/code/TeamRPG-App/rpg-skills-matrix/web' is not indexed. Please index it first using the index_codebase tool.

● This is odd - the status says it's indexed, but search disagrees. This looks like a bug in the MCP indexing server where the status and search are out of sync. Let me try clearing and re-indexing:

● claude-context - clear_index (MCP)(path: "/home/mjh/code/TeamRPG-App/rpg-skills-matrix/web")
  ⎿  No codebases are currently indexed or being indexed.                                                                                                                                                                                              

● There's clearly a bug with the MCP indexing server. Here's what's happening:

  1. Index appears to complete: Status shows "✅ fully indexed" with 191 files and 3334 chunks
  2. Search immediately fails: Says "not indexed"
  3. Clear confirms: "No codebases are currently indexed"

  This suggests the index isn't persisting between operations - possibly the MCP server is crashing, restarting, or not saving the index to disk properly.

  Why This Happened

  The MCP claude-context server appears to have an issue where:
  - The indexing process reports success
  - But the index data isn't actually available for search queries
  - This could be a memory issue, persistence bug, or the server process restarting

Steps to Reproduce

Fresh install with latest Claude Code on WSL2 Arch Linux

Claude Model

Not sure / Multiple models

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.0.25

Platform

Anthropic API

Operating System

Other Linux

Terminal/Shell

WSL (Windows Subsystem for Linux)

Additional Information

_No response_