Make incremental indexing and snapshot publication atomic

[TheGreenCedar]

Parent: #899

Finding

The live incremental database, edge resolution, grounding snapshots, and search snapshots do not share one commit boundary. A cancellation or late error can publish a graph state that no completed run owns.

Evidence

• crates/codestory-runtime/src/lib.rs:10718
• crates/codestory-indexer/src/lib.rs:1084
• crates/codestory-store/src/storage_impl/mod.rs:1192
• Full refresh already stages and promotes a separate database

Acceptance Criteria

• Incremental work writes to an isolated staging/savepoint boundary.
• Projection, cleanup, resolution, semantic docs, and derived snapshots finalize before publication.
• Cancellation/error discards staging and leaves last-known-good state readable.
• Publication has one durable generation/run identity.
• Fault injection covers every transition.
• The v0.14.3 incomplete-run compatibility marker migrates safely.

Verification

• Crash/cancel matrix across every phase
• Concurrent readers see only old or fully new generation
• Full and incremental fidelity/regression suites
• Repo-scale timing evidence

Non-Goals

• Do not retain partial-success semantics for production publication.
• Do not rewrite the graph contracts unnecessarily.

Metadata

• Release: v0.15.0
• Area: Index architecture
• Priority: P1
• Wave: Next

Implementation Slices

• Stage incremental graph and grounding snapshots before live publish #936 - staged incremental core database and grounding snapshots
• Persist durable index publication generation identity #941 - durable publication generation and run identity
• Publish persisted search by core generation #943 - generation-scoped persisted search publication
• Finalize semantic documents before core publication #945 - staged semantic document completion
• Serve the last complete publication during concurrent refresh #946 - serve the last complete publication during concurrent refresh
• Complete the atomic publication crash and cancellation matrix #955 - complete the remaining publication crash/cancel transition matrix
• Record post-publication repo-scale timing evidence #956 - record post-implementation repo-scale timing evidence

Workstreams

• Stage incremental graph and grounding snapshots before live publish #936 — stage incremental graph and grounding snapshots
• Persist durable index publication generation identity #941 — persist publication generation identity
• Publish persisted search by core generation #943 — publish persisted search by core generation
• Finalize semantic documents before core publication #945 — finalize semantic documents before core publication
• Complete the atomic publication crash and cancellation matrix #955 — complete crash and cancellation matrix
• Reopen published storage after cross-process refresh lock handoff #975 — reopen storage after cross-process refresh handoff
• Record post-publication repo-scale timing evidence #956 — record post-publication repo-scale timing evidence