fix(indexer): record non-code files on the SCIP path so cgc index stops reporting a partial index - #1566

Fixes #1565 — reported by a user indexing a 46-file C# project with scip-dotnet, where cgc index . said "Repository '.' has only 32 of 46 files indexed. Continuing." on every run and never converged.

Full suite: 1080 passed, 7 skipped, no failures.

Cause

Two rules counted files, and one could never be satisfied.

The expected count comes from estimate_processing_time → discover_files_to_index, which returns supported extensions plus a generic set (discovery.py:14-22): .md .txt .json .yaml .yml .toml .ini .cfg .sh .bat .ps1, plus Dockerfile, Makefile, .gitignore, .dockerignore, .env.

The actual count is File nodes in the graph.

The gap was scip_pipeline.py, in the supplementary Tree-sitter pass:

ts_parser = get_parser(repo_file.suffix)
if not ts_parser:
    continue          # no File node, no record, nothing

The Tree-sitter pipeline has no such hole — pipeline.py:189 falls back to add_minimal_file_node, and parse_file separates the two cases deliberately so it can: generic types return "unsupported": False (graph_builder.py:1048) while genuinely unparseable ones return True (:1053).

So the two pipelines disagreed about what counts as a file, and the SCIP path was short by exactly the number of non-code files in the repo.

Reproduction

files on disk:                      46
discover_files_to_index (expected): 46
  with a .cs parser:                32
  with NO parser:                   14   (.gitignore, Dockerfile, LICENSE.txt,
                                          README.md, appsettings.json, build.sh, …)
SCIP path writes File nodes for:    32

The 32/46 split is the natural one for a project of that shape, not a coincidence.

Fix

Give the SCIP path the same fallback. Non-code files now get a minimal File node, count toward job progress, and are surfaced in the summary log:

[SCIP+TS] Recorded 14 non-code file(s) as minimal File nodes

Test

tests/unit/tools/test_scip_pipeline_minimal_nodes.py pins the two pipelines to the same contract: for a 32-source + 14-non-code repo, File nodes written must equal files discovered.

Reverting the fix fails it with the reported symptom:

AssertionError: graph would hold 32 File nodes but discovery expects 46
                — `cgc index` will warn on every run

Notes for review

• Impact was cosmetic in graph terms — the C# code was always fully indexed, and the missing entries are inert placeholder nodes. The real cost was that a false partial-index warning is indistinguishable from a genuine one, so an actual failure would have been invisible.
• Only the SCIP path was affected, so behaviour differed by language for the same repository.
• Related but separate: bug(indexer): SCIP job progress exceeds 100% (observed 400%) and reports negative time remaining when SCIP covers only part of the repo #1535 (SCIP job progress can exceed 100% because total_files is snapshotted before this supplementary pass). This PR makes processed include minimal nodes, which is consistent with that count once bug(indexer): SCIP job progress exceeds 100% (observed 400%) and reports negative time remaining when SCIP covers only part of the repo #1535 is fixed.

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