feat(index): report per-file indexing failures via skipped[] + logfile (Stage 2/B2-B4)

[DeusData]

feat(index): report per-file indexing failures via skipped[] + logfile (Stage 2/B2-B4)

index_repository silently dropped files that failed to index: CBMFileResult.has_error
was set but never read, oversized files (>100 MB) were dropped with no signal, and
read/extract failures only bumped a logged-only counter — a file that couldn't be
indexed just vanished from the graph.

Collect and surface them:

• New retained {path, reason, phase} error list on struct cbm_pipeline (mirrors the
  excluded_dirs pattern) + accessor + a back-pointer on cbm_pipeline_ctx_t so both
  extraction paths can append. Wired in BOTH the sequential (pass_definitions) and
  parallel (per-worker, merged lock-free) paths — small repos take the sequential
  path, so wiring only one would leave the guard vacuous.
• Feeds: read-fail, extract-fail, the newly-CONSUMED has_error (parse timeout /
  parse failed, with error_msg), and oversized. The cross_lsp phase is reserved for
  the crash supervisor (Track C) and not fed here (the cross-LSP passes are
  best-effort with no failure return; feeding the no-source case would be false
  positives).
• MCP/CLI response gains top-level "skipped_count" (0 on clean) and, when >0, a
  capped "skipped":{files[<=50],count,truncated} + "logfile". Status stays "indexed"
  — a reported skip is the expected, handled outcome, not a degradation.
• Per-run logfile (full uncapped list) written ONLY when >=1 file is skipped:
  $CBM_INDEX_LOG override else <cache_dir>/logs/-.log.
• Generous env-configurable caps (src/foundation/limits.c): CBM_MAX_FILE_BYTES,
  default raised 100 MB -> 512 MiB; over-cap files are REPORTED (phase oversized) +
  WARNed, never silently dropped.

Reproduce-first: tests/test_index_resilience.c (gating) — an oversized file (cap
lowered via env) must appear in skipped[] with the 2 good files still indexed and a
logfile written; a clean run has skipped_count 0 and no logfile. Genuine guard:
no-op'ing the recorder makes the oversized file silently vanish (RED). Full suite
5750/0, no ASan/UBSan.

Part of the resilient-indexing effort (Track B surfacing layer). Refs #668.