Enhance agentic developer with code indexing

[OriNachum]

Use
https://github.com/johnhuang316/code-index-mcp

To index code as part of setup.
Consider commit, or pre-preparation for next component works

[OriNachum]

Code-index-MCP doesn't fit
I wrote my own indexer

https://github.com/teabranch/agentic-code-indexer/tree/redesign