@cavelang/cli 0.35.0 → 0.36.1

package/README.md

@@ -3,8 +3,19 @@
 The `cave` command — the whole stack behind one binary. Runs directly from
 TypeScript sources in the workspace; npm releases contain emitted JavaScript.
 
-The supported Node.js lines are 22, 24, and 26: 22.18.0 is the exact minimum,
-24.18.0 Active LTS is recommended, and 26.4.0 Current is also tested. Linux,
+The shared CAVE text reader requires valid UTF-8 in files and standard input.
+Malformed bytes produce a filename or stdin diagnostic instead of silently
+becoming replacement characters. `parse`, `add` and `import` return status 1
+without stdout on this decoding error; invalid additions/imports leave existing
+history unchanged, and `add` rejects the input before creating a missing database.
+Explicit replacement characters, accented text and emoji remain valid input.
+Action execution and doctor share hook-file validation: configuration must be
+valid UTF-8 JSON mapping nonblank names to command strings, with no unpaired
+surrogates in names or commands. Invalid configuration fails before action
+effects; doctor reports the failure without revealing configuration contents.
+
+The supported Node.js lines are 24 and 26: 24.16.0 and 26.1.0 are their exact minimums,
+24.21.0 Active LTS is recommended, and 26.8.2 Current is also tested. Linux,
 macOS, and Windows are supported; CI represents them with Ubuntu 24.04, macOS
 15, and Windows Server 2022 and exercises the CLI's native, filesystem,
 process, and built-package paths on each.
@@ -57,6 +68,14 @@ The source modules remain separate private workspace packages for focused
 ownership and tests. See [the package migration table](../../PACKAGE_SURFACES.md)
 when updating an import from a former standalone package name.
 
+The CLI build checks literal runtime imports in its published `dist/src` and
+`dist/internal` trees after consolidation. External package roots must appear
+in the CLI's dependencies, optional dependencies or peer dependencies; a private
+workspace's development dependency alone is insufficient. Diagnostics identify
+the importing file and package. Compiled tests are excluded. Computed import
+names, package-local aliases, export targets and actual dependency availability
+still require the installed-package smoke checks.
+
 ## Commands
 
 ### JSON compatibility
@@ -70,6 +89,12 @@ replace any nested database rows with the same claim record and never expose
 `claim_key`, `raw_line`, or `value_text` columns. New optional fields may be
 added within a version; incompatible shape changes require a new version.
 
+Query parse failures exit with status 1 and write diagnostics to stderr, leaving
+stdout empty even with `--json`. Filter line numbers count blank and comment
+lines in the supplied query; separate positional arguments join with newlines.
+Confidence thresholds must be finite. Correcting a failed query requires no
+database rebuild or recovery.
+
 `cave parse --json` is the parser AST/debug surface, not a persisted claim
 record. `cave export` remains canonical CAVE text (with optional `;@` identity
 annotations), which is the language interchange contract rather than JSON.
@@ -92,42 +117,55 @@ plan against an empty in-memory store when no store exists yet.
 
 All commands—synchronous, asynchronous, and long-running—enter through one
 promise-based dispatcher. It owns argument-exception formatting, stdout and
-stderr routing, exit codes, and SIGINT/SIGTERM propagation. Servers, watchers,
+stderr routing, exit codes, and SIGINT/SIGTERM propagation. An already-aborted
+runtime signal stops dispatch before argument normalization, command loading,
+or command-specific I/O; dispatch returns quietly with code 0, while the process
+wrapper retains signal exit codes. Servers, watchers,
 timers, protocol readers, and stores finish their cleanup before a signal exit
 is reported. Unexpected errors are one-line and stack-free by default; set
 `CAVE_DEBUG=1` to include the diagnostic stack.
 
+Ingestion cancellation also interrupts pending URL requests and response reads.
+SIGINT exits with code 130 after cleanup, without reporting cancellation as an
+unexpected error; strict ingestion leaves the target unchanged.
+
 | Command | Flags | Behavior |
 |---|---|---|
 | `parse [file…]` | `--json` | Lint (stdin by default). Exit 1 when diagnostics exist; `--json` dumps the AST document. |
 | `highlight [file…]` | | ANSI syntax colors from the tree-sitter grammar's own highlight query (see [`@cavelang/highlight`](../highlight)); `cave export` colors the same way on a terminal. |
 | `add [--db p] [file…]` | `--strict`, `--check`, `--no-prelude`, `--no-src` | Ingest. Lenient by default (problems on stderr, valid lines land); `--strict` rolls back on any problem; `--check` is the shape gate (spec §20.3) — the append rolls back if it introduces new expectation violations; `--no-prelude` starts from an empty registry instead of the standard §5.5 pairs. Claims without a `@src:` context are stamped `@src:cli` (spec §9.5); `--no-src` opts out. |
 | `import [--db p] [file…]` | `--strict`, `--no-prelude` | Restore/merge a database from CAVE text — `add` minus provenance stamping, because canonical text *is* the interchange format and replayed claims must keep their exported claim keys (spec §9.5). |
-| `query [--db p] <pattern…>` | `--json`, `--limit <n>`, `--cursor <t>`, `--all`, `--aliases`, `--as-of <t>`, `--at <t>`, `--resolve`, `--sources`, `--no-prelude` | Bounded CAVE-Q page (100 matches by default, maximum 1,000). Extra positionals join as lines, so `WHERE` filters ride as separate arguments. Bindings print as `?x = value`, followed by `  ; comment` when the matched claim carries one (a multi-line comment opens as `;` lines above the binding line, as it does above a claim), so evidence written next to a claim travels with the answer; fully bound patterns print the matched raw line, comment block included (or the pattern itself for transitive matches, which carry no row). Human output ends with `next: <token>` when another page exists; pass it to `--cursor` to continue the first page's frozen transaction snapshot. `--aliases` widens matching through the §13.6 closure; `--as-of <t>` reconstructs belief at a past date/timestamp/tx (spec §12.3); `--at <t>` selects valid-time claims and interpolates trajectories (spec §32.4); `--resolve` matches only the winners the §26 resolution policy picks among contested facts (incompatible with `--all`). `--sources` overlays the store's declared sources (spec §23.4) inside a rolled-back transaction — federation-lite, nothing persists, URLs included; the answer is whole (no `--cursor`), and a text store, which followed its local sources on open, loads only its URL sources here. `--no-prelude` aligns the read-time registry with a store written via `add --no-prelude`. |
+| `query [--db p] <pattern…>` | `--json`, `--limit <n>`, `--cursor <t>`, `--all`, `--aliases`, `--as-of <t>`, `--at <t>`, `--resolve`, `--sources`, `--no-prelude` | Bounded CAVE-Q page (100 matches by default, maximum 1,000). Extra positionals join as lines, so `WHERE` filters ride as separate arguments. Bindings print as `?x = value`, followed by `  ; comment` when the matched claim carries one (a multi-line comment opens as `;` lines above the binding line, as it does above a claim), so evidence written next to a claim travels with the answer; fully bound patterns print the matched raw line, comment block included (or the pattern itself for transitive matches, which carry no row). Human output ends with `next: <token>` when another page exists; pass it to `--cursor` to continue the first page's frozen transaction snapshot. A historical-row or lineage change rejects the cursor; restart without `--cursor`. `--aliases` widens matching through the §13.6 closure; `--as-of <t>` reconstructs belief at a past date/timestamp/tx (spec §12.3); `--at <t>` selects valid-time claims and interpolates trajectories (spec §32.4); `--resolve` matches only the winners the §26 resolution policy picks among contested facts (incompatible with `--all`). `--sources` overlays the store's declared sources (spec §23.4) inside a rolled-back transaction — federation-lite, nothing persists, URLs included; the answer is whole (no `--cursor`), and a text store, which followed its local sources on open, loads only its URL sources here. `--no-prelude` aligns the read-time registry with a store written via `add --no-prelude`. |
 | `search [--db p] <terms…>` | `--raw`, `--limit <n>`, `--json`, `--no-prelude` | FTS5 full-text search over the store's index (spec §13.2): subject, verb, object, attribute name, value text, comment, and the raw line as written, so tags, contexts, and inverse spellings match too. The terms are one literal phrase by default (hyphenated names such as `token-expiry` are safe); `--raw` passes FTS5 MATCH syntax through (`AND`/`OR`/`NOT`, `NEAR`, `prefix*`, column filters such as `comment:heap`). Newest first, one raw line per match with its comment; `--limit` defaults to 100 (maximum 1,000) and a trailing `more matches beyond <n>` line reports a cap. `--json` emits a `cave.search/v1` object whose matches are `cave.claim/v1` records. Superseded and retracted rows stay searchable (spec §9.6); confirm currency with `query`. |
 | `resolve [--db p]` | `--aliases`, `--policy`, `--json`, `--no-prelude` | Contested facts under the §26 resolution policy: every fact more than one belief series speaks about, candidates ranked (precedence class, reliability-weighted confidence, tx) with the winner first — what `query --resolve` would match. `--policy` prints the effective policy instead: the built-in precedence ladder merged with in-band `source/<name> HAS precedence:` / `HAS reliability:` declarations. |
-| `derive [--db p] [rules.cave…]` | `--dry-run`, `--full`, `--aliases`, `--min-conf <p>`, `--max-passes <n>`, `--list`, `--retract <r>`, `--json`, `--no-prelude` | Declare and fire rules (spec §24, see [`@cavelang/rules`](../rules)): `premises => conclusion` forward chaining over current beliefs, `BECAUSE`/`VIA` lineage, watermark-incremental and idempotent; retracts conclusions whose premises no longer hold. |
+| `derive [--db p] [rules.cave…]` | `--dry-run`, `--full`, `--aliases`, `--min-conf <p>`, `--max-passes <n>`, `--list`, `--retract <r>`, `--json`, `--no-prelude` | Declare and fire rules (spec §24, see [`@cavelang/rules`](../rules)): `premises => conclusion` forward chaining over current beliefs, `BECAUSE`/`VIA` lineage, watermark-incremental and idempotent; retracts conclusions whose premises no longer hold. Declaration errors exit nonzero in both text and JSON modes. Pass exhaustion exits nonzero, reports `complete: false` in JSON and labels the final text summary `derived (incomplete)`. |
 | `act [--db p] <name> [p=v…]` | `--declare`, `--list`, `--retract <n>`, `--dry-run`, `--no-check`, `--aliases`, `--hooks <file>`, `--json`, `--no-prelude` | Execute an action template (spec §25, see [`@cavelang/act`](../act)): validate parameters, check CAVE-Q preconditions against current belief, append effects atomically with lineage inside the §20.3 shape gate; out-of-band hooks fire after commit. |
-| `automate [--db p]` | `--once`, `--declare`, `--list`, `--retract <n>`, `--hooks <file>`, `--agent <template>`, `--json`, `--no-prelude` | The event-driven loop (spec §29, see [`@cavelang/automate`](../automate)): in-band `automation/<name>` trigger patterns over new claims fire rules, actions, out-of-band hooks and agent prompts; `--once` for cron, `--declare`/`--list`/`--retract` for the lifecycle; the daemon polls `MAX(tx)` and settles on change. |
+| `automate [--db p]` | `--once`, `--declare`, `--list`, `--retract <n>`, `--hooks <file>`, `--agent <template>`, `--json`, `--no-prelude` | The event-driven loop (spec §29, see [`@cavelang/automate`](../automate)): in-band `automation/<name>` trigger patterns over new claims fire rules, actions, out-of-band hooks and agent prompts; `--once` for cron (nonzero on incomplete settling or failures), `--declare`/`--list`/`--retract` for the lifecycle; the daemon polls `MAX(tx)` and settles on change. |
 | `check [--db p]` | `--stale <days>`, `--json`, `--no-prelude` | Knowledge health report (spec §20, see [`@cavelang/shape`](../shape)): shape violations against in-band `EXPECTS` declarations, stale current beliefs (default horizon 90 days), review candidates (conf 0.3–0.7), alias disagreements, coverage stats. Exit 1 on violations; everything else is advisory. |
 | `backup [--db p] --out <file>` | `--force`; `--verify <file>`, `--sha256 <hex>` | Create an online, exact snapshot of the store, verify it, and publish it atomically; or verify a prior snapshot (spec §13.2.2). |
 | `restore <snapshot> --db <path>` | `--force`, `--sha256 <hex>` | Verify and atomically restore exact snapshot bytes; refuses active/stale WAL, SHM, and rollback-journal sidecars (spec §13.2.2). |
 | `generate [--db p]` | `--out <file>`, `--version <n>`, `--no-prelude` | Deterministic versioned TypeScript interfaces and store-backed readers from current `EXPECTS` claims (spec §20.4, see [`@cavelang/shape`](../shape)); embeds normalized schema and SHA-256, fails on ambiguous/unsupported expectations before writing. |
-| `suggest-alias [--db p]` | `--min <s>`, `--limit <n>`, `--agent <template>`, `--timeout <s>`, `--write`, `--json`, `--no-prelude` | Alias discovery (spec §27, see [`@cavelang/shape`](../shape)): same-entity candidates from string/graph similarity as suggested `ALIAS` claims at review-band confidence (0.3–0.5). Prints pipeable CAVE text; `--write` appends stamped `@src:suggest/alias`; `--agent` runs an LLM judge over the candidates (the ingest/eval shell contract). Pairs with any recorded `ALIAS` history are never re-suggested. |
-| `sync [--db p] <source>` | `--as <label>`, `--into <label>`, `--dry-run`, `--no-record`, `--json`, `--no-prelude` | Store merge (spec §28, see [`@cavelang/sync`](../sync)): another CAVE store file — or `;@`-annotated canonical text, `-` for stdin — merges by row identity; present rows skip, re-runs merge nothing, effective merges append a `SYNCED-INTO` record (`--no-record` for checkouts, spec §28.6). |
-| `export [--db p]` | `--out <file>`, `--current`, `--tx`, `--max-sensitivity <level>`, `--no-prelude` | Sensitivity-scoped canonical CAVE text (spec §9.7) — default maximum `internal`; select `restricted` for complete portable history or a replica. `--current` compacts but never sanitizes permanent history (§9.6). `--tx` precedes every claim line with its `;@` transaction annotation (spec §28.4). Stdout by default; `--out` writes a file and reports the claim count. |
+| `suggest-alias [--db p]` | `--min <s>`, `--limit <n>`, `--agent <template>`, `--timeout <s>`, `--write`, `--json`, `--no-prelude` | Alias discovery (spec §27, see [`@cavelang/shape`](../shape)): `--min` requires a finite score in 0..1 or a percentage and `--limit` a positive safe integer. Returns same-entity candidates from string/graph similarity as suggested `ALIAS` claims at review-band confidence (0.3–0.5). Prints pipeable CAVE text, reversing the undirected relation when necessary to preserve entity names; an unrepresentable pair reports an error. `--write` validates each fresh line against its proposed pair before appending stamped `@src:suggest/alias`; `--agent` runs an LLM judge over the candidates (the ingest/eval shell contract). Pairs with any recorded `ALIAS` history are never re-suggested; writes recheck both directions under the transaction reservation and skip reviewed pairs. `--json` returns an array; `--json --write` writes and returns `{ suggestions, appended }`, with the selected proposals and actual appended count. |
+| `sync [--db p] <source>` | `--as <label>`, `--into <label>`, `--dry-run`, `--no-record`, `--json`, `--no-prelude` | Store merge (spec §28, see [`@cavelang/sync`](../sync)): another CAVE store file — or `;@`-annotated canonical text, `-` for stdin — merges by row identity; matching present rows skip, conflicting identities reject the source with a nonzero exit, re-runs merge nothing, effective merges append a `SYNCED-INTO` record (`--no-record` for checkouts, spec §28.6). |
+| `export [--db p]` | `--out <file>`, `--current`, `--tx`, `--max-sensitivity <level>`, `--no-prelude` | Sensitivity-scoped canonical CAVE text (spec §9.7) — default maximum `internal`; select `restricted` for complete portable history or a replica. `--current` compacts but never sanitizes permanent history (§9.6). `--tx` precedes every claim line with its `;@` transaction annotation, including a JSON provenance payload when contexts cannot reconstruct stored dimensions (spec §28.4). Stdout by default; `--out` writes a file and reports the claim count. |
 | `report [--db p] [template…]` | `--out <file>`, `--aliases`, `--resolve`, `--as-of <t>`, `--at <t>`, `--max-sensitivity <level>`, `--no-prelude` | Render sensitivity-scoped cited Markdown from fenced and inline CAVE-Q templates (spec §9.7, §31, see [`@cavelang/view`](../view)). Every query uses the same audience, alias, resolution, transaction-time, and valid-time snapshot options. |
-| `serve [--db p]` | `--port <n>`, `--host <a>`, `--max-sensitivity <level>`, `--no-prelude` | The sensitivity-scoped human read surface (spec §9.7, §30, see [`@cavelang/view`](../view)): one static page whose counts, aliases, history, lineage, and search are computed only from visible rows. Strictly read-only (GET only), localhost by default. |
+| `serve [--db p]` | `--port <n>`, `--host <a>`, `--max-sensitivity <level>`, `--no-prelude` | The sensitivity-scoped human read surface (spec §9.7, §30, see [`@cavelang/view`](../view)): one static page whose counts, aliases, history, lineage, and search are computed only from visible rows. Strictly read-only (GET/HEAD only), localhost by default. |
 | `mcp [--db p]` | `--read-only`, `--permissions <list>`, `--tools <list>`, `--hooks <file>`, `--no-prelude`, `--src <ctx>`, `--no-src` | Serve the engine as an MCP server on stdio (see [`@cavelang/mcp`](../mcp)) — static tools for version-matched help plus add/query/fuse/search/about/neighbors/reconstruct/derive/export/lint, and one generated `act_<name>` tool per current action. Permission classes separate `read`, ephemeral `evaluate`, durable `record`, and effect-capable `action`; `--read-only` keeps only read/evaluate. Permission, tool, and read-only scopes intersect. `--hooks` supplies reviewed out-of-band commands for action tools. Appends are stamped `@src:agent/<client-name>` (spec §9.5); `--src` replaces the stamp, `--no-src` disables it. |
-| `ingest [--db p] <globs/urls…>` | `--agent <template>`, `--stdout`, `--lenient`, `--plan`, `--dry-run`, `--json`, `--no-prelude` | LLM-driven ingestion of files and web pages (fetched and readability-extracted) through any headless agent (see [`@cavelang/ingest`](../ingest)): strict atomic staging by default; explicit lenient partial progress with a complete per-source manifest; isolated URL outcomes classified as retryable network/HTTP or permanent HTTP failures; batching, hybrid context, MCP or stdout agents, incremental retry digests, and `--plan` NDJSON for SDK drivers. |
+| `ingest [--db p] <globs/urls…>` | `--agent <template>`, `--stdout`, `--lenient`, `--plan`, `--dry-run`, `--json`, `--no-prelude` | LLM-driven ingestion of files and web pages (fetched and readability-extracted) through any headless agent (see [`@cavelang/ingest`](../ingest)): strict atomic staging by default; explicit lenient partial progress with a complete per-source manifest; isolated URL outcomes classified as retryable network/HTTP or permanent HTTP failures; batching, hybrid context, MCP or stdout agents, incremental retry digests, and `--plan` NDJSON for SDK drivers. Execution `--json` cannot be combined with `--plan` or `--dry-run`. |
 | `eval <suite…>` | `--agent <template>`, `--judge <template>`, `--runs <n>`, `--stdout`, `--min <p>`, `--json`, `--no-prelude` | Golden-fixture extraction/query evals (see [`@cavelang/eval`](../eval)): N fresh-store runs against any agent, claim-key + value scoring with §9.5 actor-stamp normalization, CAVE-Q expectations, optional LLM judge, `--min` CI gate. |
 | `connect [<source>]` | `--map <file\|inline>`, `--key <field>`, `--sql <query>`, `--watch`, `--prune`, `--query <pattern>`, `--dry-run`, `--list`, `--no-prelude` | Deterministic structured ingestion (spec §9.8, §23, see [`@cavelang/connect`](../connect)): CSV/TSV/JSON/JSONL/SQLite/URL records through `?field` templates (a file, or inline as a comma-separated list of claim lines), `--sql` reshaping any tabular source through a temporary SQLite table first, physical source identity and CSV/TSV/JSONL line spans, per-record digests, `--watch`, `--prune`, query-time overlay. Without a source, the store's declared sources run (spec §23.4): `source/<name> HAS path: …` claims with `map`, `key`, `format`, `delimiter`, `table`, `sql`, and `records` attributes mirror the options, a `.cave` path needs no map, and paths resolve against the store's directory; `--list` prints them, `--name` selects one, `--query` overlays them all, `--watch` re-runs on any of their files. A CAVE text file used as `--db` follows its declared sources on every open. |
 | `reconstruct [--db p] <seed…>` | `--query <text>`, `--agent <template>`, `--steps <n>`, `--claims <n>`, `--timeout <s>`, `--trace`, `--no-prelude` | Active memory reconstruction from seed cues (spec §18, see [`@cavelang/loop`](../loop)): best-first traversal collecting related claims as canonical CAVE text; the heuristic policy by default, an LLM select/stop policy with `--agent`. |
-| `doctor [--db p]` | `--hooks <file>`, `--json` | Read-only runtime, package-layout, configuration, and store-health diagnostics. Missing optional configuration is advisory; unsupported runtimes, broken assets, malformed configured hooks, and unreadable or corrupt stores fail. Reports identify configuration sources but never expose paths, hook content, URLs, or environment values, so both human and `cave.doctor/v1` JSON output are safe to share. |
+| `doctor [--db p]` | `--hooks <file>`, `--json` | Read-only runtime, package, configuration and store-health checks. See [Diagnosis](#diagnosis) for results, snapshot behavior and privacy. |
 | `demo` | | The cave-loop multi-hop recovery demo (§18). |
 | `version` | | Print the cave version. |
 | `help [command]` | | The overview, or one command's options and examples. |
 
+File output from `export`, `report`, `generate` and `backup` cannot target the
+source database or its SQLite `-wal`, `-shm` and `-journal` files. The check
+includes database symlinks, existing file aliases and resolved output-parent
+directories, including sidecars that SQLite has not created yet. Text stores
+retain protection for their source file without reserving SQLite sidecar names.
+
 All query-time arguments share one UTC parser. For example,
 `--at 2026-07-02T12:00:00` and `--at 2026-07-02T12:00:00Z` select the same
 instant on every host; explicit numeric offsets such as `+02:00` are honored.
@@ -145,6 +183,91 @@ Shape declarations may add `#cardinality:one` or an attribute
 `#unit:<unit>` tag. `cave check` reports the observed count and normalized
 units when those constraints fail; declarations without either tag keep the
 compatible one-or-more presence check.
+The text coverage summary rounds average confidence to a whole percent, using
+`<1%` or `>99%` when rounding would otherwise imply zero or certainty.
+`cave check --json` retains the numeric average; when no current positive
+beliefs remain, the JSON average is null and the text omits it.
+Health-report text appends findings iteratively, so large violation, stale,
+review and alias-disagreement sections do not exceed JavaScript's
+function-argument limit. A regression checks all 130,000 review candidates
+and retains the successful exit status for advisory findings. Reports still
+assemble in memory; this is not a finding-count or output-memory budget.
+`cave resolve --policy` likewise calculates table width iteratively. Large
+sets of source declarations retain complete, aligned policy rows without
+exceeding JavaScript's function-argument limit; the policy and output remain
+in memory.
+Resolution text rounds reliability and effective confidence to one decimal
+percent, using `<0.1%` and `>99.9%` when rounding would otherwise imply zero
+or certainty. Exact zero and one remain `0%` and `100%`; JSON retains numbers.
+
+## Diagnosis
+
+Use doctor to check an installation and store without repairing or migrating it:
+
+```sh
+cave doctor --db knowledge.db
+cave doctor --db knowledge.db \
+  --hooks hooks.json --json
+```
+
+A normal diagnosis returns status 0 when no checks fail, including when warnings
+remain, or status 1 when a check fails. Missing optional configuration is
+advisory. Unsupported runtimes, broken package assets, malformed configured
+hooks, and unreadable or corrupt stores fail. Read each failed check's remediation
+before retrying; doctor does not perform the repair for you.
+
+A readable schema-version-0 database without `cave_` or `idx_cave_` objects
+is reported as uninitialized. Unrelated names such as `caveat` do not imply
+a CAVE migration; existing CAVE prefixes are recognized without regard to case.
+
+For current-schema SQLite stores, the database checks cover:
+
+| Check | What it examines |
+|---|---|
+| `store.integrity` | SQLite integrity and foreign-key references. |
+| `store.rows` | Canonical lowercase UUIDv7 row identity with `id = tx`; payload-column consistency; binary negation, importance and approximation flags; finite confidence in [0, 1]; positive finite sigma levels, with null retaining the legacy default. It also streams stored history through the row decoder to check authored values and their numeric caches, and rejects empty or non-text explicit provenance values. |
+| `store.search` | Search entries match stored claims, without missing, duplicate, orphaned or stale entries. This is separate from SQLite integrity. |
+
+The `store.rows` scan also recomputes every historical claim's key using its
+stored contexts. A mismatch fails diagnosis even when a newer revision is
+valid. Contexts are read through the claim index while history is streamed;
+diagnosis does not collect all history or repair keys. Corrected keys and
+contexts are checked again on the next invocation.
+The scan also loads stored tags and checks canonical claim emission, so
+unemittable terms, contexts or tags fail diagnosis before export or sync.
+Malformed contents remain redacted and the database is left unchanged for
+repair and retry.
+
+Stored edge roles must be `WHEN`, `VIA`, `BECAUSE` or `QUALIFIES`. Unsupported
+roles also fail `store.rows` without printing the role or changing the database;
+diagnosis checks the corrected relationships again after repair.
+
+Provenance validation covers actor, source, run and domain entries without
+printing their values or claim identities. SQLite TEXT affinity alone permits
+binary values, and SQLite integrity checks do not reject empty strings; these
+therefore belong to the semantic row check. A failed check leaves the database
+unchanged. Correct the affected data or restore a verified backup, then rerun
+doctor before retrying annotated export.
+
+SQLite diagnosis holds one read transaction across schema, integrity, row and
+search checks, so the report describes one snapshot. A subsequent invocation sees
+later commits. With rollback journaling, the read transaction can temporarily
+block a writer's commit; closing the diagnostic connection releases its locks.
+
+A database close failure adds `store.cleanup` while preserving completed checks.
+For a successfully assembled text store, this retains its claim count and does
+not mislabel cleanup failure as a parse or declared-source loading failure.
+A temporary SQLite capability-probe close failure adds `runtime.sqlite.cleanup`
+while retaining the capability result. Both are failures with redacted messages.
+
+Human-readable and `cave.doctor/v1` JSON reports identify configuration sources
+but omit paths, hook contents, URLs, claim contents and environment values,
+including when a text store or declared source cannot load. The targeted checks
+do not establish semantic correctness of every historical claim.
+
+The programmatic `diagnose({ db, hooks })` API captures both options once before
+inspection. Changing getters cannot alter the reported database configuration
+source or switch hook files during diagnosis; a later call can use new options.
 
 ## Exact backup and portable interchange
 
@@ -156,6 +279,21 @@ cave backup --verify knowledge.snapshot.db --sha256 <recorded-hex>
 cave restore knowledge.snapshot.db --db restored.db --sha256 <recorded-hex>
 ```
 
+Verify and restore the standalone snapshot produced by `cave backup`.
+Backup verification checks SQLite integrity, schema and the supplied checksum.
+It can preserve structurally valid rows with semantic errors, such as damaged
+claim keys or empty provenance. Run `cave doctor --db restored.db` to diagnose
+the restored copy before export or sync. Keeping the original snapshot allows
+repair work on the copy without changing that recovery point.
+Snapshots from schema version 1 through the current version remain recoverable.
+Verification and restore preserve their bytes and schema version; the next
+writable open migrates the restored copy, leaving the retained backup untouched.
+Unversioned and newer schema formats are rejected.
+Verification rejects sources with SQLite WAL, shared-memory or rollback-journal
+sidecars, whose contents would not be covered by a checksum of the main file.
+Backup and restore also refuse destination sidecars even with `--force`, and
+restore cannot write into a sidecar path belonging to its source snapshot.
+
 Backup is an online, consistent SQLite snapshot safe with WAL and concurrent
 readers/writers. CAVE verifies and atomically publishes it. Stop all users of
 the destination before restore; a WAL/SHM/journal sidecar makes restore refuse rather
@@ -163,6 +301,45 @@ than guess. Failed creation or restore leaves the previous destination intact.
 
 For portable, reviewable CAVE text:
 
+`export --out`, `generate --out` and `report --out` write and flush a temporary
+file in the destination directory before atomically replacing the output.
+Write, flush, file-close or rename failures leave an existing output intact.
+Export decoding errors, including conflicting historical payload columns and
+invalid confidence or sigma levels, return status 1 with the affected claim ID and no partial stdout.
+Annotated export rejects stored claim keys that disagree with the claim and
+its contexts, so replay cannot silently change the belief series associated
+with a transaction. It also rejects empty or non-string stored provenance values
+before producing a replay file. Existing output
+files and database bytes remain unchanged, and absent output files stay absent.
+Sensitivity filtering still applies before decoding: excluded malformed rows do
+not prevent a narrower export. Repair the included row before retrying a complete
+export.
+Cleanup attempts both file closure and temporary-file removal. Multiple failures
+are retained in operation order rather than allowing cleanup to hide the first
+error. If the output did not exist, these publication failures leave it absent;
+the same command can be retried after the filesystem failure is resolved.
+If temporary-directory cleanup fails after replacement, the complete file
+remains published, but the command returns status 1 without a success message.
+The error explicitly identifies the published output and temporary directory,
+and retains the cleanup failure as its cause. Inspect the complete output and
+the named temporary directory before deciding whether another export is needed.
+Existing permission bits
+are retained; valid symlinks are followed without replacing the link, while
+hard-link aliases retain the old file. Dangling symlinks and non-regular files
+are refused. Replacement requires write access to the destination directory.
+This protects against partial output writes; it does not promise persistence
+of the directory rename across power loss. Shell redirection (`>`) retains the
+shell's ordinary truncation behavior.
+
+If `report` throws while generating a stored citation, it exits with status 1,
+names the affected claim in stderr and emits no report to stdout. An existing
+`--out` file stays intact and a new output path stays absent, including when
+earlier queries in the template succeeded. Retry after resolving the evidence
+failure. Ordinary template/query problems still produce diagnostic Markdown
+and status 1; that complete diagnostic document can be written to `--out`.
+Invalid report `--at` or `--as-of` options fail before reading templates or
+opening the store and leave the output unchanged, even for a static template.
+
 ```
 $ cave export --db knowledge.db --max-sensitivity restricted --out backup.cave
 exported 812 claim(s) to backup.cave
@@ -192,8 +369,43 @@ accidental secret ingest, rotate it, stop sync, rebuild a reviewed safe store,
 then explicitly destroy or expire every affected copy with the relevant
 storage provider's confirmation.
 
+`cave sync --json` emits a report on stdout for successful merges and rejected
+claim/annotation content; a nonempty `problems` array also sets exit status 1.
+Source-access, UTF-8 and database failures instead produce stderr diagnostics
+and empty stdout with status 1. Check status and available stdout before parsing
+JSON, including for dry runs. Correcting the source allows a fresh preview and
+retry against the same target.
+If final store closure fails after a report is produced, stdout retains that
+JSON, stderr adds the cleanup diagnostic, and status is nonzero. A completed
+merge may already be committed even when the command exits with a failure.
+
 Everything is testable without spawning: individual buffered commands expose
 `(argv) → { code, out, err }`, while `dispatch(argv, runtime)` exercises the
 same awaited path as the binary with injectable streams and an abort signal.
 `main.ts` only hands process arguments to `runCli` and assigns its final exit
 code.
+
+Buffered commands that own a store wait for their work to finish, then attempt
+store close once. A close failure preserves completed `out` and existing `err`,
+appends a `store close failed` diagnostic, and changes a successful status to 1;
+an existing nonzero status is retained. Operation errors become ordinary failure
+output before cleanup, so a later close failure cannot hide them. This covers
+ingestion, queries (including async source overlays), search, resolution,
+derivation, actions, checks, backup, alias suggestions, sync, reports, export,
+client generation and reconstruction. Async source or agent work settles before
+its store closes. Completed writes, generated files and published snapshots are
+not undone by final-close failure; query overlays still roll back their scratch
+writes. A close attempt does not guarantee release when native close fails.
+Within these owned-store wrappers, thrown values that cannot be printed use
+`[unprintable thrown value]`. Formatting failures cannot skip the close attempt,
+erase completed output, or hide a simultaneous cleanup failure. This applies
+to synchronous commands and awaited source-query work.
+The outer dispatcher uses the same safe formatting for unexpected exceptions.
+Debug output captures a stack once; if reading or formatting it fails, the
+dispatcher falls back to the message, then the unprintable-value placeholder.
+Normal diagnostics do not read the stack. A formatting failure therefore cannot
+replace the command's status-1 diagnostic with a rejected dispatch promise.
+The command-level catches for backup, restore, alias suggestion and
+reconstruction use the same placeholder for unreadable setup failures, including
+file inspection before a store is owned. Direct programmatic calls retain their
+ordinary `{ code, out, err }` failure result in those cases.

package/dist/internal/act/action.js

@@ -179,7 +179,8 @@ export const parse = (subject, body) => {
     const effectTexts = [];
     for (const segment of splitSegments(rightText)) {
         const { effect, problems: effectProblems } = parseEffect(segment, bound);
-        problems.push(...effectProblems);
+        for (const problem of effectProblems)
+            problems.push(problem);
         if (effect !== undefined) {
             effects.push(effect);
             effectTexts.push(Rule.normalizeSegment(segment));

package/dist/internal/act/action.js.map

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package/dist/internal/act/declare.d.ts.map

@@ -1 +1 @@
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package/dist/internal/act/declare.js

@@ -18,6 +18,7 @@
  * wins, whoever appended it.
  */
 import { Claim, Key, Value } from '@cavelang/core';
+import { canonicalizeText } from '@cavelang/canonical';
 import { parseDocument } from '@cavelang/parser';
 import { Rule } from '@cavelang/cli/rules';
 import { Row } from '@cavelang/store';
@@ -40,20 +41,24 @@ const declarationKey = (subject, attribute) => Key.of(Claim.of({
  * decide whether a disabled declaration matters.
  */
 export const currentAttribute = (store, subject, attribute) => {
-    let winner;
-    for (const row of store.currentBeliefs()) {
-        if (row.subject === subject && row.verb === 'HAS' && row.attribute === attribute &&
-            (winner === undefined || winner.tx < row.tx)) {
-            winner = row;
-        }
-    }
-    return winner;
+    // The newest row across all series is necessarily current in its own series.
+    // Keep disabled rows in this contest: a newer retraction/negation must win.
+    return store.db.prepare(`SELECT * FROM cave_claim
+    WHERE subject = ? AND verb = 'HAS' AND attribute = ?
+    ORDER BY tx DESC LIMIT 1`).get(subject, attribute);
 };
 const enabled = (row) => row !== undefined && row.conf > 0 && row.negated === 0 && row.value_text !== null;
+/** Decode enabled action metadata without coercing malformed SQLite values. */
+const storedText = (row) => {
+    if (typeof row.value_text !== 'string') {
+        throw new TypeError(`stored action field ${JSON.stringify(row.attribute)} value_text must be text (claim ${JSON.stringify(row.id)})`);
+    }
+    return Row.parseValue(row.value_text).raw;
+};
 /** Current positive action declaration rows, newest series winner per subject. */
-const currentActionRows = (store) => {
+const currentActionRows = (rows) => {
     const bySubject = new Map();
-    for (const row of store.currentBeliefs()) {
+    for (const row of rows) {
         if (row.verb !== 'HAS' || row.attribute !== Action.actionAttribute ||
             Action.actionName(row.subject) === undefined) {
             continue;
@@ -76,7 +81,7 @@ export const loadAction = (store, name) => {
     if (!enabled(row)) {
         return undefined;
     }
-    const parsed = Action.parse(subject, Row.parseValue(row.value_text).raw);
+    const parsed = Action.parse(subject, storedText(row));
     if (!parsed.ok) {
         return { problems: parsed.problems };
     }
@@ -92,41 +97,48 @@ export const loadAction = (store, name) => {
 /** The hook name the action currently references, if any (§25.4). */
 export const currentHook = (store, subject) => {
     const row = currentAttribute(store, subject, Action.hookAttribute);
-    return enabled(row) ? Row.parseValue(row.value_text).raw : undefined;
+    return enabled(row) ? storedText(row) : undefined;
 };
-/** Parameter doc — the comment of `action/<name>/<param> IS param` (§25.1). */
-const paramDoc = (store, subject, param) => {
-    let winner;
-    for (const row of store.currentBeliefs()) {
-        if (row.subject === `${subject}/${param}` && row.verb === 'IS' && row.object === 'param' &&
-            row.negated === 0 && row.conf > 0 && (winner === undefined || winner.tx < row.tx)) {
-            winner = row;
+/** Current positive actions of a store, in declaration order. */
+export const listActions = (store) => {
+    const rows = store.currentBeliefs();
+    const docs = new Map();
+    const hooks = new Map();
+    for (const row of rows) {
+        if (row.verb === 'IS' && row.object === 'param' && row.negated === 0 && row.conf > 0) {
+            const seen = docs.get(row.subject);
+            if (seen === undefined || seen.tx < row.tx)
+                docs.set(row.subject, row);
+        }
+        if (row.verb === 'HAS' && row.attribute === Action.hookAttribute) {
+            const seen = hooks.get(row.subject);
+            if (seen === undefined || seen.tx < row.tx)
+                hooks.set(row.subject, row);
         }
     }
-    return winner?.comment ?? undefined;
+    return currentActionRows(rows).map(row => {
+        const text = storedText(row);
+        const parsed = Action.parse(row.subject, text);
+        const params = parsed.ok ?
+            parsed.action.params.map(name => {
+                const doc = docs.get(`${row.subject}/${name}`)?.comment ?? undefined;
+                return { name, ...doc === undefined ? {} : { doc } };
+            }) :
+            [];
+        const hookRow = hooks.get(row.subject);
+        const hook = enabled(hookRow) ? storedText(hookRow) : undefined;
+        return {
+            subject: row.subject,
+            name: Action.actionName(row.subject),
+            text,
+            ...row.comment === null ? {} : { description: row.comment },
+            params,
+            ...hook === undefined ? {} : { hook },
+            ok: parsed.ok,
+            problems: parsed.ok ? [] : parsed.problems
+        };
+    });
 };
-/** Current positive actions of a store, in declaration order. */
-export const listActions = (store) => currentActionRows(store).map(row => {
-    const text = Row.parseValue(row.value_text).raw;
-    const parsed = Action.parse(row.subject, text);
-    const params = parsed.ok ?
-        parsed.action.params.map(name => {
-            const doc = paramDoc(store, row.subject, name);
-            return { name, ...doc === undefined ? {} : { doc } };
-        }) :
-        [];
-    const hook = currentHook(store, row.subject);
-    return {
-        subject: row.subject,
-        name: Action.actionName(row.subject),
-        text,
-        ...row.comment === null ? {} : { description: row.comment },
-        params,
-        ...hook === undefined ? {} : { hook },
-        ok: parsed.ok,
-        problems: parsed.ok ? [] : parsed.problems
-    };
-});
 const indentOf = (line) => line.length - line.trimStart().length;
 const isStructural = (line) => {
     const body = line.trim();
@@ -169,6 +181,13 @@ export const declareActions = (store, text) => {
     const problems = [];
     const actions = [];
     const preludeLines = [];
+    const preludeSourceLines = [];
+    const addPrelude = (lines, at) => {
+        lines.forEach((line, index) => {
+            preludeLines.push(line);
+            preludeSourceLines.push(at + index);
+        });
+    };
     const declarations = [];
     // Top-level blocks: a structural unindented line plus what follows it.
     // A declaration's structural children would silently re-attach to the
@@ -180,7 +199,7 @@ export const declareActions = (store, text) => {
             blocks.push({ lines: [line], at: index + 1 });
         }
         else if (blocks.length === 0) {
-            preludeLines.push(line);
+            addPrelude([line], index + 1);
         }
         else {
             blocks[blocks.length - 1].lines.push(line);
@@ -189,7 +208,7 @@ export const declareActions = (store, text) => {
     for (const block of blocks) {
         const declaration = asDeclaration(block.lines[0]);
         if (declaration === undefined) {
-            preludeLines.push(...block.lines);
+            addPrelude(block.lines, block.at);
             continue;
         }
         if (block.lines.slice(1).some(isStructural)) {
@@ -197,17 +216,26 @@ export const declareActions = (store, text) => {
             continue;
         }
         declarations.push({ declaration, at: block.at });
-        preludeLines.push(...block.lines.slice(1));
+        addPrelude(block.lines.slice(1), block.at + 1);
     }
     return store.transaction(() => {
+        store.registry();
         let prelude = 0;
         const preludeText = preludeLines.join('\n');
         if (preludeText.trim() !== '') {
+            // Validate even cached input: older versions cached failed preludes too.
+            const canonical = canonicalizeText(preludeText, store.registry());
+            if (canonical.problems.length > 0) {
+                for (const problem of canonical.problems)
+                    problems.push({
+                        ...problem, line: preludeSourceLines[problem.line - 1] ?? problem.line
+                    });
+                return { declared: 0, unchanged: 0, prelude: 0, actions, problems };
+            }
             const digest = Rule.digestOf(preludeText);
             const known = store.currentBelief(declarationKey(preludeSubject, preludeDigestAttribute));
             if (known === undefined || known.conf <= 0 || known.value_text !== digest) {
-                const result = store.ingest(preludeText, { source: 'cave-act' });
-                problems.push(...result.problems);
+                const result = store.insertResult(canonical, { source: 'cave-act' });
                 prelude = result.ids.length;
                 store.ingest(`${preludeSubject} HAS ${preludeDigestAttribute}: ${digest} @${provenanceContext}`);
             }
@@ -217,7 +245,8 @@ export const declareActions = (store, text) => {
         for (const { declaration, at } of declarations) {
             const parsed = Action.parse(declaration.subject, declaration.body);
             if (!parsed.ok) {
-                problems.push(...parsed.problems.map(message => ({ line: at, message })));
+                for (const message of parsed.problems)
+                    problems.push({ line: at, message });
                 continue;
             }
             const action = parsed.action;
@@ -250,12 +279,12 @@ export const declareActions = (store, text) => {
  */
 export const retractAction = (store, ref) => {
     const subject = Action.actionSubject(ref);
-    const rows = store.currentBeliefs().filter(row => row.subject === subject && row.verb === 'HAS' && row.attribute === Action.actionAttribute &&
-        row.negated === 0 && row.conf > 0);
-    if (rows.length === 0) {
-        return { ok: false, error: `no current action matches ${JSON.stringify(ref)}` };
-    }
     return store.transaction(() => {
+        const rows = store.currentBeliefs().filter(row => row.subject === subject && row.verb === 'HAS' && row.attribute === Action.actionAttribute &&
+            row.negated === 0 && row.conf > 0);
+        if (rows.length === 0) {
+            return { ok: false, error: `no current action matches ${JSON.stringify(ref)}` };
+        }
         for (const row of rows) {
             store.insertResult({
                 claims: [{ claim: { ...store.toClaim(row), conf: 0, raw: '', comment: 'retracted: cave act --retract' }, line: 0 }],