bug: rules_engine.index_skip_files directory globs (**/phaser/**) skip entire project, and skip stays sticky without --rebuild #453

Describe the bug

Two related problems with the new rules_engine.index_skip_files config field (added in v0.11.1 via #447):

1. Directory-style globs over-match and skip the entire project. A pattern like **/phaser/** causes cora index to skip all 152 files (not just the phaser directory), indexing 0 symbols.
2. The skip appears "sticky": after removing the .cora.yaml (so no skip list is active), a plain incremental cora index still reports all files as skipped. Only cora index --rebuild recovers.

To reproduce

Project: hompimpah, 152 files.

(1) Glob over-match

cat > .cora.yaml <<'YAML'
rules_engine:
  index_skip_files:
    - "**/phaser/**"
YAML
cora index
# → ✅ Indexed 0 symbols from 0 files (152 skipped, 0 errors)
# Expected: skip only files under any phaser/ directory, index the rest.

Also reproduced with "**/templates/quiz-adventure/**" and "**/engine/**" — every directory-glob pattern skipped the whole project. File-specific patterns (ularTanggaScene.ts) were not tested for correctness because of problem (2).

(2) Sticky skip after config removal

rm .cora.yaml          # no skip list active anymore
cora index             # incremental
# → ✅ Indexed 0 symbols from 0 files (152 skipped, 0 errors)   ← still skipped!
cora index --rebuild   # only this recovers
# → ✅ Indexed 582 symbols from 152 files (0 skipped, 0 errors)

Confirmed: no CORA_* env vars set, no .cora.yaml lingering, global ~/.codecora/config.{json,toml} unchanged.

Expected

• Directory globs (**/phaser/**) should match only files within a phaser/ directory, not every file in the project.
• Incremental cora index should re-evaluate the current config on each run; removing the skip list should restore full indexing without needing --rebuild.

Likely cause

1. Glob matcher may treat a leading/trailing **/ as match-any-path, or the pattern is matched against the full path in a way that ** greedily consumes everything.
2. The incremental index path likely caches the skip decision (or the file manifest) in the DB and does not invalidate it when the config changes.

Environment

• cora 0.11.1 (release that introduced index_skip_files)
• macOS arm64