indexer: when the parser library cannot initialise, source files are silently dropped and the job reports completed #1746

Summary

We indexed a set of repositories. Every job reported completed with errors: [], but the graph
contained no Function/Class nodes and no File nodes for any source file: only generic files
(md/yml/json) were stored. Nothing was logged. The cause was environmental (tree-sitter-language-pack
refused a cache directory owned by another uid), but CGC reported success. #913 was the same
"hollow graph reported as success" symptom with a different cause.

Cause

1. utils/tree_sitter_manager._load_tree_sitter_dependencies probes
   get_language('python') (L58). Any exception (here tree_sitter_language_pack.DownloadError: Refusing to use cache directory … owned by uid 0, not … uid 1000) is caught by
   except (ImportError, Exception) (L66). The code then falls back to tree_sitter_languages,
   which is not installed, and raises "tree-sitter and tree-sitter-language-pack are required …
   pip install codegraphcontext[parsing]". The original error survives only as
   __cause__.__context__, and the advice points at packages that are already installed.
2. graph_builder.get_parser catches that and returns None (L144-148). parse_file returns
   {"unsupported": True} (L494-496).
3. The pipeline writes nothing for unsupported files (pipeline.py L183-197: minimal File nodes are
   only for generic files). The job ends completed, and failed_files in the index summary is 0.
4. The warning goes through warning_logger. That is suppressed at the default
   ENABLE_APP_LOGS=CRITICAL and never reaches stderr or mcp_debug.log.

The same silent completed happens when the grammar download fails (issue #1745).

Expected

A parser that cannot initialise for a supported extension should fail the job, or at least add an
errors[] entry and a failed_files count, and surface the original exception text. #1616 added
a non-empty-bundle assertion to the golden tests, but it would not catch this: the graph is not
empty.

Environment

codegraphcontext 0.6.13 (same on main), tree-sitter-language-pack 1.20.0, Python 3.12, container
with the grammar cache owned by root and the process running as uid 1000.

Disclosure: the investigation and this report were prepared with AI assistance (Claude Code) and reviewed by a human before posting.