Full index can stall in symbol extraction and exit with E013_INDEX_EXTRACTION_STALLED

[Widthdom]

Summary

While working on issues #1669, #1735, and #1753 from origin/main, a full repository refresh with the locally built Debug binary stalled and exited with E013_INDEX_EXTRACTION_STALLED.

Reproduction observed

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

The run progressed through most files, then reported no extraction progress for five minutes and exited with:

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

A retry with lower parallelism also failed to complete:

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

That run stopped after repeated progress messages around tests/CodeIndex.Tests/QueryCommandRunnerTests.cs (symbols) and ended with Error: command cancelled before it could complete.

Expected

Full index refresh should either complete or report a file/phase-specific actionable error without preventing the documented agent workflow from refreshing the local index.

Notes

A quick Open Issue search for E013_INDEX_EXTRACTION_STALLED found no existing duplicate.

[Widthdom]

Work started on branch codex/fix-issue1604-2744.