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Full index can stall on current repository after branch refresh #2717

Description

@Widthdom

Summary

While working on issues #1694, #1422, #1702, and #2013 from a fresh branch based on origin/main, a full local index refresh failed with the stall guard.

Reproduction observed

Repository: Widthdom/CodeIndex
Branch base: origin/main @ 0a803d7
Machine: macOS arm64, .NET SDK 10.0.100

Commands attempted:

dotnet ./src/CodeIndex/bin/Debug/net8.0/cdidx.dll . --json

Result:

E013_INDEX_EXTRACTION_STALLED
Index extraction made no progress for 5m 0s (0 files processed).
Last active phase included src/CodeIndex/Indexer/References/Languages/SqlReferenceExtractor.cs (symbols).

A second attempt with lower parallelism also did not complete:

dotnet ./src/CodeIndex/bin/Debug/net8.0/cdidx.dll . --json --parallelism 1

That run progressed farther but ended with:

Error: command cancelled before it could complete.

Expected

A full repository index refresh should complete or produce a narrower actionable file/phase diagnostic that does not leave the workspace without a fresh index.

Notes

This was discovered during unrelated help/completion documentation work. I did not include a fix in that PR to keep its scope limited.

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