Refactor AGENTS.md from encyclopedia to map; move spec into docs/

Splits the 990-line AGENTS.md into a 184-line map (architecture,
where-to-find index, always-on invariants, capability matrix,
maintenance contract) plus 18 new docs/*.md files holding the deep
content per topic (storage, schema and query languages, indexes,
embeddings, branches/commits, runs, merge, changes, execution, policy,
server, CLI reference, audit, errors, CI, constants, v0.3.1 notes).

Adds scripts/check-agents-md.sh and a check_agents_md CI job that
verifies every docs/ link in AGENTS.md resolves and every doc in the
canonical set is linked. CLAUDE.md remains a symlink to AGENTS.md.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

docs/merge.md

@@ -0,0 +1,30 @@
+# Merging (three-way) and Conflicts
+
+`exec/merge.rs`.
+
+## Strategy
+
+Ordered, row-by-row cursor merge:
+
+- `OrderedTableCursor` scans each table sorted by `id` and supports peek/pop matching.
+- `StagedTableWriter` buffers `MERGE_STAGE_BATCH_ROWS = 8192` rows into a temp Lance dataset (`OMNIGRAPH_MERGE_STAGING_DIR`).
+- The merge runs per sub-table; results are published as one atomic manifest update.
+
+## Outcome enum
+
+`MergeOutcome { AlreadyUpToDate | FastForward | Merged }`
+
+## Conflict types (`error.rs`)
+
+```
+MergeConflictKind:
+  DivergentInsert        // same id inserted on both branches
+  DivergentUpdate        // updated differently on both branches
+  DeleteVsUpdate         // one side deletes, other updates
+  OrphanEdge             // edge references a node deleted by the other side
+  UniqueViolation
+  CardinalityViolation
+  ValueConstraintViolation
+```
+
+Returned as `OmniError::MergeConflicts(Vec<MergeConflict { table_key, row_id?, kind, message }>)`. The HTTP server surfaces this as a 409 with structured `merge_conflicts[]` (top 3 + "+N more").