[aft-alfonso]

This is the 0.64 index-store cutover. Text search, the call graph and meaning search move to one index store per repository, shared by its worktrees and clones; the old trigram index, SQLite call-graph store and content-addressed views are deleted (about 215,000 lines net).

What changes for users

• Each repository builds its new indexes once on first use: text in about a second, the call graph in under a minute for large projects. Worktrees of one repository share them, and a new worktree starts from a sibling's indexes and processes only the files that differ.
• Meaning search reuses old vectors for unchanged files embedded with the same model.
• Old index folders stay on disk; npx @cortexkit/aft cache prune-legacy lists and removes them.
• views.enabled, views.callgraph_copies and worktree.ram_overlay show a removal notice; views.idle_checkout_hours becomes idle.checkout_hours. Config names retired in 0.62 or earlier are refused in user config and load with a notice in project config.
• trace_to and impact label each root (main, test, attribute, public API, no caller found).

Measured on AFT's own repository (7,300 files)
Call-graph build 207 s to 17 s; index disk 1.7 GB to 0.3 GB; typical edit catch-up 4.7 s to 0.1 s; dead code first run 72 s / +4.25 GB to 6-8 s / +0.8 GB; an edited worktree's call graph median 3 MiB between publications; a new worktree at the same commit under a second instead of about 160 CPU-seconds.

Verification

• Full Rust suite on Linux: all pass except the 12 native-secret-shell tests and one rust-analyzer test the build server can't run (both fail the same way on main).
• Incremental call graph equals a cold build after each of 430 real edits (edit, reuse, extract and checkout gates).
• Dead-code findings unchanged across a 91-project corpus; search-quality benchmark rows byte-identical except five declared pattern-lane candidate counts (land-index-store-0.64.json).
• macOS and Windows compile with warnings as errors.

The release notes are in review; the version bump and tag follow through scripts/release.sh after this merges.

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Summary by cubic

This is the 0.64 index-store cutover: text search, the call graph, meaning search, dead code and TODO counts all move to one index store per repository, shared by its worktrees and clones. The old trigram index, SQLite call-graph store and views are deleted (about 215,000 lines net). The data layer is always on: there is no development switch, and configure no longer builds or opens today's indexes at all.

What changes for users

• Each repository builds its new indexes once on first use; worktrees share them, and a new worktree starts from a sibling's indexes and processes only the files that differ.
• Meaning search reuses stored vectors for unchanged files embedded with the same model, and a repository is filled by one process at a time so no chunk is embedded twice.
• Editing a config file (Cargo.toml, tsconfig.json, package.json) rebinds only the files it changed: crate roots, found config files and workspace package names are tracked per name, not per workspace member walk.
• write, edit and apply_patch return before the edited file's syntax tree is built: search sees the edit at once, and the call graph parses it on its next refresh.
• A repository whose index-store files a newer build wrote is refused with storage_requires_newer_reader, naming the file and version, instead of being rebuilt over them; a store an older build published still serves text while the checkout's own bind rebuilds its call graph, and a read-only bind that still fails waits a minute before retrying.
• A call-graph build or refresh a read asked for is admitted to its pool immediately instead of waiting behind a queued maintenance job, so concurrent reads no longer answer callgraph_building while the build sits queued.
• Old index folders stay on disk; npx @cortexkit/aft cache prune-legacy lists and removes them, and status no longer sizes them.
• views.enabled, views.callgraph_copies and worktree.ram_overlay show a removal notice; views.idle_checkout_hours becomes idle.checkout_hours.
• Config names retired in 0.62 or earlier are refused in user config; a project config carrying one still loads, translating the name with a notice.
• Configure's missing-tool and language-server warnings take their file list from the index-store checkout instead of walking the project once it has published; the same list feeds the background TODO refresh.
• trace_to and impact follow callers to real roots and label each root: main, test, attribute, public API, or no caller found.
• Index-store background work (builds, meaning fills, refreshes) runs in process-wide pools, so a fill round waiting on the embedding backend no longer holds every other root's builds and tool calls; all call-graph engines resolve on one shared thread pool.
• When a root's index store fails to build or refresh, the daemon's health report names the root and its reason code instead of a count.
• Minified bundles (*.min.js, or JS/CSS with almost no line breaks) are still searched by grep, but are not parsed for the call graph, cut into meaning-search chunks, or counted as files the call graph fails to cover.
• Dead code and unused exports run on the index store's own integer graph, with per-file facts extracted at index time; TODO counts come from stored markers, and both list their files from the store's checkout instead of walking the project. A member kept alive by a test-code call is now a test seed, a call like service.render() resolves to the exact method, and a Python dotted import no longer records an unresolved call site.
• Automatic dead code and unused exports follow their own schedule: they wait for a published call graph, run on one root at a time, and at most once every 30 minutes while edits arrive.
• aft_search reads each candidate file once per search, no longer serializes concurrent searches' query embeddings, matches file-name searches against the index's path list instead of walking the project, and again carries each symbol hit's caller count and caller files from the store's current call graph.
• A worktree that has stopped publishing no longer keeps every segment it ever read in the store: another checkout's publication copies what the idle one still reads into one segment and drops the rest, and meaning-search vector segments are combined into one once a repository has more than eight of them.

Measured and verified

• On AFT's own repository (7,300 files): call-graph build 207 s to 17 s, index disk 1.7 GB to 0.3 GB, typical edit catch-up 4.7 s to 0.1 s, new worktree at the same commit under a second instead of about 160 CPU-seconds, and a busy worktree's call graph holds about a tenth of the memory after a broad edit (about 120 MB instead of 1 GB).
• The store keeps at most 1,024 index files open and one descriptor per segment file, so busy daemons stay below macOS's open-file limit; a busy worktree's piled-up index changes are folded into one segment without rereading or reparsing any file (under a second on 7,000 files, where the rebuild took about 12 s and over 1 GB); decoded call-graph files share a 256 MB bounded cache; the segment block cache shards by block and serves hits under a read lock (43 ns per warm hit on one thread, 357 ns each on twelve); a finished build returns its freed pages to the allocator, so resident memory settles near the working set; the memory census carries the meaning fill's own timings into daemon health, and the health rollup reuses a checkout's memory figure until its recorded changes, refresh or publication move its epoch or 30 seconds pass.
• A publication carries the call-graph engine that built it, so the refresh after an edit reuses it instead of building a new one; on 430 replayed edits one engine served all 88 publications, using about a third less CPU. A refresh never holds decoded copies of files it only checks: a crate-root edit held about 360 MB instead of 1.5 GB.
• A refresh publishes once 256 files have been re-resolved since the last publication, so a broad edit's re-resolved files are released instead of being held until the checkout goes quiet.
• Incremental call graph equals a cold build after each of 430 real edits; search-quality benchmark rows byte-identical except five declared pattern-lane candidate counts.
• Replaying 6,956 recorded callers/call_tree/trace replies through the new store matches main's corpus except 34 reviewed differences (C++ type-matched method calls, macro-template calls and macro-generated self calls now resolve).
• Full Rust suite passes on Linux except the 12 native-secret-shell tests and one rust-analyzer test the build server can't run (both fail the same way on main); macOS and Windows compile with warnings as errors.

^{Written for commit a4df3b3. Summary will update on new commits.}