feat(indexer): baseline + overlay incremental indexing architecture

[jafreck]

Summary

Add incremental indexing to Lore using a baseline + overlay architecture so the index stays accurate during active editing — including multi-agent concurrent-writer scenarios — without blocking on a full SCIP rebuild after every change.

Closes #212

Design document: docs/incremental-index-design.md

Schema Changes

• Add layer (baseline|overlay) and generation columns to all data tables (files, symbols, symbol_refs, type_refs, symbol_relationships, file_imports, annotations, symbol_metrics, external_deps)
• Add dirty_files table tracking files with active overlay data
• Add reverse_deps table for impact-set computation ("file X is depended on by files Y, Z")
• Add effective_* SQL views that merge baseline + overlay layers, preferring overlay for dirty files
• New lore_meta keys: generation, generation_pending, baseline_head_sha, overlay_head_sha
• Helper functions: getGeneration(), incrementGeneration()

Pipeline Changes

• PipelineContext gains layer and generation fields
• ScipIndexerStage: only runs in baseline builds, writes layer='baseline' with generation
• SourceIndexStage: overlay mode writes layer='overlay', preserves baseline rows; only deletes prior overlay rows
• LspEnrichmentStage: cross-file enrichment for overlay mode only; baseline builds skip LSP for SCIP-covered languages
• ResolutionStage: resolveSymbolEdges() accepts overlayOnly option to scope name-based resolution to overlay refs
• New ReverseDepsStage: builds/updates reverse_deps from resolved imports + refs
• New OverlayCleanupStage: atomic baseline promotion — deletes old generation, clears promoted overlay rows, rebuilds reverse_deps
• IndexBuilder.baselineRebuild(): new method for background SCIP reconciliation with atomic promotion

Watcher/Poller Changes

• Immediate flushes are overlay-only (tree-sitter + LSP enrichment, no SCIP)
• Deferred SCIP flush replaced with baselineRebuild() after quiet period
• scipQuietPeriodMs now controls background baseline rebuild scheduling

Resolution Taxonomy

• Add overlay_stale resolution method for refs invalidated by file changes but not yet re-enriched

MCP Tool Freshness

• FreshnessInfo type: { source: 'baseline'|'mixed'|'overlay', baseline_age_s, dirty_file_count }
• getFreshness() helper in read-only.ts
• Automatically injected into every MCP tool response via loggedHandler

Invariants

1. Baseline is always complete — after a successful build, every file has baseline rows
2. Overlay never deletes baseline — overlay rows coexist with baseline rows for the same file
3. dirty_files is authoritative — a file has active overlay data iff it appears in dirty_files
4. Generations are monotonic — lore_meta.generation only increases
5. Cross-layer refs resolve by name — falls back to name-based lookup when callee_id doesn't exist in effective symbols

Test Results

All 1830 tests pass (98 test files, 0 failures).

[codecov]

Codecov Report

❌ Patch coverage is 96.92308% with 6 lines in your changes missing coverage. Please review.
✅ Project coverage is 87.54%. Comparing base (b39a1f3) to head (9316b11).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
src/indexer/stages/source-index.ts	91.42%	6 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #213      +/-   ##
==========================================
+ Coverage   87.43%   87.54%   +0.11%     
==========================================
  Files          82       84       +2     
  Lines        9429     9579     +150     
  Branches     2925     2958      +33     
==========================================
+ Hits         8244     8386     +142     
- Misses       1185     1193       +8     

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