Fix rag init context cancel

[gtardif]

Allow to ctrl-C or kill nicely docker-agent when it's using RAG with long-running initialisation

[docker-agent]

Review Summary

Assessment: 🟢 APPROVE

Summary

This PR successfully implements context cancellation support for RAG initialization, allowing graceful shutdown with ctrl-C or kill signals. The implementation follows Go best practices:

✅ Context Threading: Context parameter properly threaded through the entire call chain from top-level functions (Initialize, CollectFiles, DirectoryTree) down to helper functions (addPathToWatcher)

✅ Cancellation Checks: All context checks use proper select statements with context.Done() and default cases to prevent blocking

✅ Loop Protection: Context checks in file iteration loops prevent runaway operations during long-running directory traversals

✅ Test Coverage: New test file collect_cancellation_test.go includes both cancellation and timeout scenarios

✅ Backward Compatibility: All existing callers updated to pass context, including test files using t.Context() which is the correct pattern

The changes are well-structured and address the stated goal of allowing graceful shutdown during long-running RAG initialization.

Findings

No bugs found in the changed code.