Fix potential inconsistencies when removing schemas with references

[jviotti]

Signed-off-by: Juan Cruz Viotti jv@jviotti.com

[cubic-dev-ai]

No issues found across 6 files

[augmentcode]

🤖 Augment PR Summary

Summary: This PR hardens incremental indexing when schemas are removed in the presence of cross-schema references.

Changes:

• In the Combine phase, detects deleted dependencies.metapack entries and rebuilds dependents.metapack for schemas that were referenced by the removed schema.
• Adds BuildState::raw_disk_entry() to read prior on-disk entries even when they’ve been marked deleted in the overlay.
• Adds BuildState::deleted_keys() so delta planning can enumerate removed output keys.
• Computes a removed_entries set for outputs belonging to schemas no longer present, and uses it to propagate dirtiness through dependency graphs.
• Simplifies “potential stale output” detection to !removed_entries.empty().
• Adds CLI regression tests for (1) removing a referenced schema (expected failure) and (2) removing a referencing schema (expected dependents rebuild).

Technical Notes: The change relies on per-schema /%/dependencies.metapack graphs to identify cross-schema relationships even when the owning schema’s outputs are being disposed.

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[github-actions]

Benchmark Index (community)

Details

Benchmark suite	Current: 076bbbe	Previous: 63171c9	Ratio
Add one schema (0 existing)	22 ms	22 ms	1
Add one schema (100 existing)	42 ms	39 ms	1.08
Add one schema (1000 existing)	192 ms	208 ms	0.92
Add one schema (10000 existing)	2002 ms	2012 ms	1.00
Update one schema (1 existing)	20 ms	21 ms	0.95
Update one schema (101 existing)	39 ms	44 ms	0.89
Update one schema (1001 existing)	209 ms	225 ms	0.93
Update one schema (10001 existing)	2291 ms	2307 ms	0.99
Cached rebuild (1 existing)	11 ms	11 ms	1
Cached rebuild (101 existing)	13 ms	13 ms	1
Cached rebuild (1001 existing)	30 ms	33 ms	0.91
Cached rebuild (10001 existing)	244 ms	259 ms	0.94

This comment was automatically generated by workflow using github-action-benchmark.

[github-actions]

Benchmark Index (enterprise)

Details

Benchmark suite	Current: 076bbbe	Previous: 63171c9	Ratio
Add one schema (0 existing)	19 ms	19 ms	1
Add one schema (100 existing)	32 ms	31 ms	1.03
Add one schema (1000 existing)	163 ms	136 ms	1.20
Add one schema (10000 existing)	1709 ms	1406 ms	1.22
Update one schema (1 existing)	18 ms	18 ms	1
Update one schema (101 existing)	32 ms	30 ms	1.07
Update one schema (1001 existing)	178 ms	157 ms	1.13
Update one schema (10001 existing)	2141 ms	1760 ms	1.22
Cached rebuild (1 existing)	10 ms	10 ms	1
Cached rebuild (101 existing)	11 ms	11 ms	1
Cached rebuild (1001 existing)	26 ms	23 ms	1.13
Cached rebuild (10001 existing)	199 ms	162 ms	1.23

This comment was automatically generated by workflow using github-action-benchmark.