[Bug]: When used as MCP one can't reindex.

[vjache]

Bug Description

Hi there!
Nice project!
I tried to use it with Kilo, and seems everything fine except that when I try in parallet terminal use 'cie index', then it raises error, seems due to it can't acess to the DB. Also there is no tool in MCP to do that.
So I wonder how to you use this solution, may be I don't get something?

Steps to Reproduce

1. Run some AI IDE (e.g. Kilo) with MCP cie configured in mcp.json
2. Open another terminal and try 'cie index'

Expected Behavior

I'd expect the successful result as if I run 'cie index' without cie-MCP running in parallel.

Actual Behavior

Error: Cannot initialize indexing pipeline
Cause: Failed to open or initialize the database
Fix: Try 'cie reset' to rebuild the database, or close other CIE instances

Operating System

macOS

CIE Version

v0.7.20

Go Version

go1.26.0

Relevant Logs

Error: Cannot initialize indexing pipeline
Cause: Failed to open or initialize the database
Fix:   Try 'cie reset' to rebuild the database, or close other CIE instances

Additional Context

No response

Checklist

• I have searched for existing issues that describe this bug
• I am using the latest version of CIE