@c4a/context-cli 0.6.1 → 0.6.3

package/providers/context/resources/manuals/reference/project-api.md

@@ -0,0 +1,825 @@
+---
+id: context.sdk.project-api
+kind: procedure
+mediaType: text/markdown
+---
+
+# Project API
+
+Import from `@c4a/context` in `src/index.ts`.
+
+## `defineProject`
+
+```ts
+import { defineProject } from "@c4a/context";
+
+export default defineProject({
+  sources: [],
+  phases: [],
+  packages: [],
+});
+```
+
+The project file is executable TypeScript, but the preferred style is a small
+declaration list. Put heavy logic in imported transform files.
+
+## Sources
+
+A source is a stable knowledge boundary, not only a display label. Repo, file,
+and Lark sources use a date batch plus a concrete module name; multiple code or
+document modules may share the date. The flattened selector `YYYYMMDD/module`
+is the source identity used by phases, snapshot paths, and source refs.
+Codegraph NodeRef/ViewRef and knowledge paths use the stable module name without
+the date:
+
+```text
+knowledge/<collection>/<slug>.md
+knowledge/<collection>/<containment>/<slug>.md  # only for an intentional hierarchy
+knowledge/codegraph/<module>/symbol/<slug>.md
+repo:<date>/<module>#symbol:...
+file:<date>/<module>/<document>#span:...
+lark:<date>/<module>/<document>#span:...
+capture:file:<date>/<module>
+align:lark:<date>/<module>:architecture
+dist/<source-name>-kb/...
+```
+
+Choose the module boundary before extraction. In a monorepo, register each
+confirmed package/subdirectory under the same date batch. A repo root that
+resolves to multiple modules is for inspection; it is not an extraction unit.
+Approved codegraph paths use the stable module name; the date remains only in
+source selectors, phase ids, and evidence refs:
+
+```text
+knowledge/codegraph/module-a/...
+knowledge/codegraph/module-b/...
+```
+
+For prose Views, provide a stable filename `slug` and omit `path`; the CLI
+derives the path. Omit `containment` when the page is an independent collection
+entry, producing `knowledge/<collection>/<slug>.md`. Set `containment` only
+when the approved structure intentionally places the page under a parent path;
+it is not a required source/module wrapper.
+
+The registry stores this as one date entry containing several `modules` entries,
+and materializes each module at `sources/repo/<date>/<module>`.
+Repo module names are project-wide codegraph identities and therefore cannot be
+reused under another date batch. Refresh an existing module through its original
+date/module selector.
+When a repo module and the Context workspace share the same Git root, the CLI
+normalizes even an absolute `--local` input into a path relative to the
+workspace and stores the package directory as `subpath`. Materialized repo
+links always use relative symlink targets. This keeps the registry and links
+valid when the whole checkout moves. Cross-repository absolute checkout roots
+remain absolute because no shared movable root can be assumed.
+The date entry must be a valid calendar date in `YYYYMMDD` form. Use
+`context source ensure <date>` or `context source inspect <date>` for the whole
+batch, and `<date>/<module>` when targeting one module.
+
+```yaml
+sources:
+  - name: "20260712"
+    modules:
+      - name: module-a
+        local: ../monorepo
+        subpath: packages/module-a
+        git:
+          remote: https://git.example.com/product/monorepo.git
+          ref: <full-commit-sha>
+      - name: module-b
+        local: ../monorepo
+        subpath: packages/module-b
+        git:
+          remote: https://git.example.com/product/monorepo.git
+          ref: <full-commit-sha>
+```
+
+File and Lark registries use the same outer shape. Their modules hold local
+document boundaries or remote document identities:
+
+```yaml
+sources:
+  - name: "20260712"
+    modules:
+      - name: local-manual
+        local: ../manual
+      - name: api-guide
+        local: ../api-guide
+```
+
+### Batch source registration
+
+Use one command when a user confirms several source modules together:
+
+```bash
+context source add batch [YYYYMMDD] --input <sources.yaml|json|-> --format json
+```
+
+The payload is a non-empty `sources` array. Every item requires `type`. Repo
+also requires `module` and accepts `local`/`remote`/`ref`. File requires `local`
+and accepts `include`; Lark accepts exactly one of `url`, `docToken`, or
+`wikiToken` plus optional `title`. File/Lark `module` is optional and is derived
+with the same lowercase path-safe rule as the single-source commands. Resolved
+module identities must be unique across the batch.
+
+Source mutations share a project write lock, and every registry file is
+replaced atomically. Never run separate `source add` processes in parallel. A
+batch executes items in order; if a runtime item fails, its error lists the
+completed items and the same payload may be rerun idempotently.
+
+```yaml
+sources:
+  - name: "20260712"
+    modules:
+      - name: user-manual
+        url: https://example.larksuite.com/wiki/example-a
+      - name: migration-guide
+        url: https://example.larksuite.com/wiki/example-b
+```
+
+### `source(name)`
+
+Reference one registered source by name. The reference is type-neutral in
+project code; each phase resolves it through the registry and checks whether it
+is a repo, file, or lark source:
+
+```ts
+import { source } from "@c4a/context";
+
+const productDocs = source("product-docs");
+```
+
+### `source(namespace, module)`
+
+Reference one registered repo module. Use the date batch and module name
+returned by `context source add repo`:
+
+```ts
+const moduleA = source("20260712", "module-a");
+const moduleB = source("20260712", "module-b");
+```
+
+These references resolve to `20260712/module-a` and `20260712/module-b`;
+extraction and verification remain independent.
+
+### `source(namespace, module, { type })`
+
+Reference one file or Lark module under a date batch:
+
+```ts
+const localManual = source("20260712", "local-manual", { type: "file" });
+const userManual = source("20260712", "user-manual", { type: "lark" });
+```
+
+These references produce module-scoped phase ids and manifest entries without
+treating the date as one document identity. Captured document files remain
+siblings under `sources/file|lark/<date>/` and share the date-level
+`manifest.json`; the logical `date/module` identity does not create another
+directory level.
+
+For a confirmed multi-document request, declare one capture phase per module.
+While any module is uncaptured, `context status --format json` selects either
+the `route.capture.configuration-required` Route with
+`workflow.current.configuration`, or the `route.capture.pending-target` Route
+with the next declared command in `workflow.current.commands`.
+
+Each command item declares its effect and availability. The current route's
+`gate` identifies the decision and authority boundary. Write commands are bound
+to the workflow revision; after one succeeds, rerun status instead of reusing
+the old command. An external command also declares
+`execution.target: agent-host`; execute it as a top-level Agent-host action so
+network and credential-store access are not lost inside a restricted child
+sandbox.
+
+### `allSources("repo")`
+
+Reference all repo sources as one collection:
+
+```ts
+import { allSources } from "@c4a/context";
+
+const repoSources = allSources("repo");
+```
+
+Use `allSources("repo")` only when the project should list every registered
+repo module. Prefer a specific `source("date", "module")` for extraction phases.
+
+## Phases
+
+Phases declare reads and writes. The runtime can inspect them, dry-run them, and
+record per-phase logs.
+
+The API exposes the current declared workflow only. Declare file/lark sources,
+capture phases, prose structure gates, source-bound compile phases, code
+extraction phases, review gates, close/build, and packages explicitly. The CLI
+then routes work through `context status`, `context run <phase-id>`, `context
+review html/apply`, `context close`, `context verify`, and `context build`.
+
+For Agent and automation output, use `context verify --format json --compact`.
+It returns deterministic groups, counts, affected-scope totals, and a few
+representative samples instead of repeating every issue. Read the complete,
+auditable issue set only when needed with `context verify --view diagnostics
+--page-size 25 --format json`; follow its executable pagination command without
+inventing overlapping file ranges.
+
+### Status declaration coverage
+
+`context status --format json --view full` includes a `declarationGraph` and
+`configurationGaps` for document workflows. Each row reports capture, align,
+compile, and Review coverage for a canonical source plus collection. Gaps are
+non-blocking before structure confirmation. Once a structure is confirmed,
+compile routing is exact: phase selection uses canonical source plus collection,
+and candidate progress remains bound to the current `structure_digest`. A
+compile phase from another collection is never used as fallback.
+
+Captured align targets that do not yet have an active confirmed structure are
+reported in `pendingStructureTargets`. They remain unfinished even when the
+currently active structures have been closed, verified, and built. Missing
+compile or Review declarations route to `needs-prose-configuration`; once the
+declarations are complete, status returns the exact align investigation command
+for the next target. A built package does not freeze the workspace or require a
+new workspace for later sources.
+
+`context status --format json` defaults to the compact workflow route, target,
+progress, counts, and aggregated diagnostics. Use `--view full` only when
+source, phase, package, and lifecycle inventories are needed for debugging.
+
+### Current-conversation managed execution
+
+`context status --managed --format json` exposes
+`executionMode: { mode: "managed", scope: "current-conversation" }` and resolves
+eligible human gates into immediate commands. The flag is deliberately absent
+from `defineProject`: callers start each workflow evaluation loop with managed
+status, then execute the returned revision-bound command unchanged. Returned
+commands carry a compact current-conversation marker instead of repeating every
+authority. A later process or conversation gets ordinary human-gated behavior
+by default.
+
+Managed Review is atomic and scope-validated:
+
+```bash
+context review approve-all <collection> --managed --format json
+context review approve-all --all --managed --format json
+```
+
+The default JSON result reports counts and change totals without listing every
+candidate id or materialized path. Add `--verbose` only when debugging requires
+the complete candidate and page details.
+
+Managed structure confirmation and Review use only the revision-bound commands
+returned by `workflow.current`. Source boundaries and unread source bodies,
+external operations, payload validation, deterministic close, and verification
+errors are never bypassed.
+
+For consecutive mechanical routes, the Agent may run:
+
+```bash
+context run --managed --until blocked-or-complete --format json
+```
+
+This is a bounded host loop over the same revisioned routes. It stops before
+read-only interpretation, project configuration, unresolved authority,
+diagnostics, or a non-unique command plan; it does not add another workflow
+entry or make semantic decisions.
+
+### `captureFile`
+
+Capture a registered file source into a committed normalized document snapshot.
+Default file capture treats `.md` files as document bodies. For MDX
+documentation sites that use `_meta.json` route metadata, declare the processor
+in `src/index.ts`:
+
+```ts
+captureFile({ source: docs, processor: mdxJsonDocs() });
+```
+
+With that processor, `.md` and `.mdx` are document bodies. Included
+`_meta.json` files are captured as route metadata assets, surfaced in
+`read-plan` / `source-index`, and mechanically projected into
+`__context_route_metadata.md` so route facts can be cited as evidence. The route
+projection records the canonical extensionless route form instead of treating a
+local `.html` URL as the source of truth.
+
+MDX component text is extracted separately: string props such as `title`,
+`label`, `description`, `href`, `to`, and component children are projected into
+`__context_mdx_component_text.md` as generated evidence. The original `.mdx`
+file remains in the snapshot unchanged. If a documentation page renders body
+text only at runtime from application code or remote data, configure that
+documentation site as an explicit source boundary instead of hand-writing route
+or body facts.
+
+```ts
+captureFile({ source: docs });
+```
+
+Phase id:
+
+```text
+capture:file:<source-name>
+```
+
+Register the source first with
+`context source add file [YYYYMMDD] --module <module> --local <path>`.
+The first registration requires `--local`; the registry may later keep `local`
+only as a refresh hint while committed snapshots remain verifiable. Multiple
+file modules may share one date. When `--module` is omitted, the CLI derives it
+from the local file or directory name.
+
+### `captureLark`
+
+Capture a registered Lark / Feishu document source into a committed normalized
+Markdown snapshot:
+
+```ts
+captureLark({ source: handbook });
+```
+
+Embedded resources are materialized with deterministic defaults. Video remains
+reference-only unless a project opts into bundling, and byte limits prevent an
+unexpected document from expanding the workspace without bound:
+
+```ts
+captureLark({
+  source: handbook,
+  resources: {
+    videos: "bundle",
+    maxBytesPerResource: 20 * 1024 * 1024,
+    maxTotalBytes: 200 * 1024 * 1024,
+  },
+});
+```
+
+Phase id:
+
+```text
+capture:lark:<source-name>
+```
+
+Register each source with
+`context source add lark [YYYYMMDD] --module <module>` and exactly one identity
+flag: `--url`, `--doc-token`, or `--wiki-token`. Multiple documents may share
+one date batch; when `--module` is omitted, the CLI derives an opaque,
+credential-safe module id. Capture reads the
+remote document through the CLI runner as structured Docx XML. Context keeps a
+redacted XML audit asset, projects supported blocks deterministically into
+readable Markdown, and materializes required inline resources such as images,
+attachments, Sheets, Bases, whiteboards, diagrams, and synced blocks. Navigation
+resources and default video capture remain explicit references. The projection
+does not infer or summarize document meaning. Its fidelity and resource reports close discovered blocks
+against converted and intentionally skipped blocks and reports evidence
+completeness separately from Markdown projection quality. Unknown non-empty XML
+blocks receive a generic, auditable, non-interactive projection and do not block
+downstream work. A remote whiteboard or diagram explicitly confirmed as deleted
+is preserved as an unavailable-resource notice with
+`document.resource.source-missing` and a warning. An embedded resource whose
+export is explicitly rejected as `authorization/permission_denied` is retained
+the same way with `document.resource.permission-denied`. Missing scopes,
+unresolved external-resource identity, retryable failures, and unclassified
+authorization errors remain evidence errors and prevent downstream Review.
+Snapshot files live under `sources/lark/<date>/` as sibling document files
+tracked by one compact date-level `manifest.json`. Each module keeps one raw
+`source.xml`, one consolidated `capture-report.json`, and its actual downloaded
+or structured resources under `assets/<module>/materialized/`; it does not emit
+one descriptor file per embedded resource. Access credentials and transient
+signed media URLs are not written into the workspace.
+
+Approved resource bytes are projected to content-addressed
+`knowledge/assets/<kind>/` paths. KB build copies selected resources to
+`others/assets/<kind>/` inside the package and rewrites page links. See
+[Lark Resource Materialization](../guides/lark-resources.md) for the complete
+resource table and storage lifecycle.
+
+Use a typed document reference in project declarations:
+
+```ts
+const handbook = source("20260712", "user-manual", { type: "lark" });
+const localDocs = source("20260712", "local-manual", { type: "file" });
+```
+
+### `alignProse`
+
+Open the prose structure gate for document evidence:
+
+```ts
+alignProse({
+  source: docs,
+  collection: "architecture",
+});
+```
+
+`collection` is an internal knowledge classification, not a package directory.
+Package build maps `codegraph`/`business`/`product` to `wikis/`,
+`architecture`/`sop`/`faq`/`decision`/`incident` to `guides/`,
+`standards`/`test` to `rules/`, and `feats` to `feats/`. The complete output
+contract is documented in [Package Outputs](../guides/package-outputs.md).
+
+When `source("name")` is type-neutral, the SDK may declare
+`align:source:<source-name>:architecture`; the CLI resolves it to
+`align:file:<source-name>:architecture` or `align:lark:<source-name>:architecture` after
+reading the registry.
+
+Align is a gated workflow. It produces and validates a structure draft, not
+final approved body:
+
+```bash
+context run align:file:<source-name>:architecture --view read-plan --format json
+context run align:file:<source-name>:architecture --view source-index --compact --format json
+context run align:file:<source-name>:architecture --view span-detail --span <source-ref> --format json
+context run align:file:<source-name>:architecture --view span-text --span <source-ref> --format json
+context run align:file:<source-name>:architecture --view existing-knowledge --query <title-or-stable-ref> --format json
+context run align:file:<source-name>:architecture --view schema --format json
+context run align:file:<source-name>:architecture --view semantic-rules --format json
+context run align:file:<source-name>:architecture --validate --input <structure.yaml> --format json
+context run align:file:<source-name>:architecture --view diagnostics --input <structure.yaml> --format json
+context run align:file:<source-name>:architecture --view structure-summary --input <structure.yaml> --format json
+context run align:file:<source-name>:architecture --stage --input <structure.yaml> --format json
+```
+
+When `workflow.current.batch` is present, several independent document slots
+can be prepared in one Agent pass and validated or staged through one command:
+
+```yaml
+schema: context.prose.structure-batch.v1
+items:
+  - phase_id: align:file:<source-a>:architecture
+    input: .tmp/agent-payloads/<source-a>-structure.yaml
+  - phase_id: align:file:<source-b>:architecture
+    input: .tmp/agent-payloads/<source-b>-structure.yaml
+```
+
+```bash
+context run --batch-input .tmp/agent-payloads/prose-structure-batch.yaml --validate --format json
+context run --batch-input .tmp/agent-payloads/prose-structure-batch.yaml --stage --managed --format json
+```
+
+Batch preflight validates every payload before writing. Stage writes ready
+slots serially; it does not merge documents or decide their semantic shape.
+
+Align results expose a recommended `payload_target.path` under
+`.tmp/agent-payloads/`. Agents should use it for transient structure inputs and
+may remove the file after a successful stage. The CLI continues to accept an
+explicit alternative path; this is an authoring convention, not validation.
+
+For the ordinary path, `read-plan` is a complete authoring packet: it includes
+the payload contract, a budgeted canonical source-ref map, exact source-body
+resources, and a direct `--stage` command. Read the bodies, author the payload,
+and run that stage command. Request `source-index` only when the packet reports
+omitted refs, and request `existing-knowledge` only when reusing or checking an
+approved identity. The separate schema and validate views are optional
+diagnostic tools, not required lifecycle steps.
+
+`--validate`, `--stage`, and `--confirm` are mutually exclusive operations. An
+`--input` without an operation is rejected unless the selected view explicitly
+consumes that input. Deterministic boundary repairs run internally before the
+result is returned. `self_healed` includes input/output Section counts, the
+number of original Sections split, and structural reason codes. Stage performs validation before writing and returns the
+same diagnostics on failure; in managed mode, a valid stage also confirms the
+structure. Successful standalone validation returns a stage command with the
+same file path. JSON run output keeps `next_action` first;
+schema and full reports stay behind explicit Views, while `--verbose` restores
+the full phase result and repeated contracts. Long diagnostics return a compact
+first page plus an exact diagnostics continuation command.
+
+Validation returns `state: ready | repair-required | invalid`. Only `ready`
+sets `valid: true` and may proceed to stage. `error_free: true` with
+`state: repair-required` means no error diagnostic remains, but a declared
+confirmation blocker still requires repair; it is not a successful result.
+
+`existing-knowledge` is the authoring-time lookup for approved identities. It
+returns stable NodeRefs, ViewRefs, titles, tags, collections, and section counts
+without exposing workspace storage paths. `--query` performs deterministic
+case-insensitive exact/prefix/substring matching; `--collection`,
+`--node-type`, `--page-size`, and the returned continuation command narrow or
+page the same View. Use it after reading source evidence and before introducing
+a new Node identity. Structure validation remains the final duplicate gate.
+
+Align and compile evidence results include `semantic_rules`. Its `required`
+array is the rule subset selected for the current judgment, with a selection
+reason and content digest for each rule. `handle`, `digest`, and
+`rules_version` are stable cache checks: reuse a loaded ruleset only while its
+content remains in the active context and both handle and digest still match.
+After context compaction, resume the paginated `semantic-rules` View for the
+returned required subset; a handle alone does not imply that the rule text is
+still available.
+
+Document evidence boundaries are deterministic rather than semantic.
+`source-index` and `chunks` mark Markdown AST blocks with
+`boundary_role: "markdown-ast-block"` and `section_candidate: true`.
+`span-text`/`span-detail` mark each returned page as
+`range_role: "transport-page"` and `section_candidate: false`; pagination line
+ranges are never structure boundaries. Structure validation blocks repeated
+fixed-width line grids that cut through AST blocks and reports sections that
+cross multiple heading paths, without classifying document topics.
+
+After capture, the capture phase itself exposes collection-neutral `read-plan`,
+`source-index`, `span-detail`, `span-text`, and other read-only evidence views.
+Status selects `route.document.classification-required` until every captured
+target has an evidence-backed, user-confirmed align declaration. Align then
+adds `schema` and `structure-summary` for structure work. Agents should not
+scan `sources/` or `.tmp` to invent evidence. They may read only the exact
+source-body files selected as required resources by the current Route; those
+files carry stable content digests and must be read in full before a receipt is
+reported. Read all required direct paths, then execute the Route's single
+`resources.after_read.command`; the CLI writes and carries the merged receipt
+set without requiring Agent-authored JSON. That acknowledgement response
+already contains the re-evaluated `workflow.current`, so no additional status
+command is needed.
+
+Generated Context Views use the same content-addressed rule. Materialization
+returns a receipt-set path and an exact post-read command. Read the complete
+file, then execute that command; unchanged content remains current across
+workflow revisions, while write and external commands still require the exact
+current revision.
+
+Compile `read-plan`, `blockers`, and `diagnostics` Views are workspace-read-only
+and may run concurrently. Compile `--validate`, compile `--stage`, structure
+confirmation, Review apply, and close are serial operations.
+
+Structure payloads use `schema_version: "context.structure.v1"` and canonical
+`file:` / `lark:` `#span` source refs. A one-file-to-one-page plan is represented
+as ordinary `nodes[]` and `views[]` in the structure. It does not bypass
+structure confirmation or compile. Continuity applies to each Section, while one View/Page may
+contain multiple independently retrievable continuous Sections. Deterministic
+boundary splitting is applied internally during validate/stage; it is not a
+separate Agent-authored payload or approval step.
+
+### `compileProse`
+
+Compile confirmed prose structure into reviewable source-bound draft pages:
+
+```ts
+compileProse({
+  source: docs,
+  collection: "architecture",
+});
+```
+
+When `source("name")` is type-neutral, the SDK may declare
+`compile:source:<source-name>:architecture`; the CLI resolves it to
+`compile:file:<source-name>:architecture` or `compile:lark:<source-name>:architecture` after
+reading the registry.
+
+Phase id:
+
+```text
+compile:file:<source-name>:architecture
+compile:lark:<source-name>:architecture
+```
+
+Compile requires confirmed CLI-managed lifecycle structure. It freezes the
+current structure for the compile round; if the user wants to change nodes,
+section ownership, or relationships, return to the align/structure gate.
+
+Common commands:
+
+```bash
+context run compile:file:<source-name>:architecture --view read-plan --format json
+context run compile:file:<source-name>:architecture --validate --format json
+context run compile:file:<source-name>:architecture --stage --format json
+context run compile:file:<source-name>:architecture --view diagnostics --format json
+```
+
+Compile validates the complete confirmed source/collection slot before writing
+any candidate, then materializes the slot atomically. Section bodies are
+source-mirrored from the confirmed spans; the Agent does not create a separate
+compile-actions payload. Each canonical source plus collection remains an
+independent structure slot. When other captured align targets remain pending,
+status routes to those slots before opening one collection-level Review
+payload. `context close` is blocked while a planned View is unprepared, still
+draft, or rejected without a structure revision.
+
+Relationships stay in `structure.yaml` typed edges in current output; compile
+does not infer relationships or inject relation markers into verbatim body.
+
+### `extractTs`
+
+Extract exported TypeScript / TSX symbols into draft candidates:
+
+```ts
+extractTs({
+  source: componentLib,
+  collection: "codegraph",
+});
+```
+
+Options:
+
+| Field | Meaning |
+|---|---|
+| `source` | `source("date", "module")` for one repo module |
+| `collection` | Code extraction uses `"codegraph"` |
+| `include` | Optional glob list inside the selected source; default is `["src/**/*.{ts,tsx}"]` |
+| `mode` | `"exports"` (default) traces public exports from automatic or configured entries; `"scan"` uses every file matched by `include` as an entry root |
+| `entries` | Optional source-relative entry files for `"exports"` mode. They override `package.json` entry detection and live only in the Context project configuration |
+| `exportedOnly` | Defaults to `true` in `"exports"` mode and `false` in `"scan"` mode |
+| `transform` | Optional markdown transform function or functions |
+
+`source` is the only package/module boundary. `include` narrows files inside
+that source; it does not select a second module. Standard packages can omit
+`entries` and use `package.json` `exports`, `main`, or `bin` detection. For a
+non-standard package, configure `entries` in the Context project instead of
+editing the source repository:
+
+```ts
+extractTs({
+  source: componentLib,
+  collection: "codegraph",
+  include: ["src/**/*.ts"],
+  entries: ["src/api.ts"],
+});
+```
+
+When the intended knowledge scope is every declaration in the selected files
+rather than a public export graph, use `mode: "scan"`. Scan mode does not accept
+`entries`; `include` supplies its file roots.
+
+Entry failures use the stable machine code `NO_ENTRY_DETECTED`. This includes
+`entries: []`, exports mode with no detected/configured entry, and scan mode
+with no files matched by `include`; these cases never succeed silently.
+
+TypeScript extraction reads the selected module's `tsconfig.json` or
+`jsconfig.json`. JSONC comments/trailing commas, local or installed `extends`,
+`compilerOptions.baseUrl`, and `compilerOptions.paths` are used for export
+tracing and internal dependency relations, so aliases such as `@/*` resolve to
+their source files.
+
+In monorepos, make each package/subdirectory a module boundary. Register the
+chosen package path with `context source add repo [YYYYMMDD] --module <module> --local <package-dir>` and
+reference it with `source("<date>", "<module>")`.
+Do not use `include` to choose a
+package from a larger monorepo source.
+
+Use `context source inspect <date>/<module>` to list detected module/package
+boundaries before choosing the source. Use `context run <phase-id> --dry-run
+--format json` to check the resolved modules, file counts, symbol counts, and
+candidate estimate before writing the ignored lifecycle candidate ledger. The dry-run
+preview also includes `knowledgeTree` and `knowledgePathExamples`, which show
+where approved Markdown will land after review apply.
+Its module and total summaries distinguish `discoveredFiles`, `analyzedFiles`,
+`skippedFiles`, `symbols`, and `relations`. Module summaries also expose the
+resolved `entryFiles`, exported/internal symbol counts, and a structural
+`candidateKinds` count. These fields describe extractor output only; the CLI
+does not infer which symbols are meaningful to a particular product or
+audience. Modules with skipped files include the deterministic traversal
+reason, such as files not reachable from exports-mode entries.
+
+Phase id shape:
+
+```text
+extract:<source-name-or-repo>:codegraph
+```
+
+Codegraph extraction has two execution policies:
+
+- `context run <phase-id>` is the Agent/user default. The first run sends every
+  code symbol to Review. Later runs preserve unchanged approved symbols and send
+  only `add`, `update`, and `remove` deltas to Review. After every phase result,
+  the Agent re-evaluates `context status --format json`; only
+  `workflow.current` decides whether Review is now required.
+- `context run <phase-id> --auto-promote` is the explicit CI/CD path. It is valid
+  only for `phase.extract.ts` codegraph phases, applies deterministic code deltas
+  without Review, refreshes deterministic close when approved knowledge changed,
+  then runs project verification. Close or verification errors make the command
+  fail; JSON output reports applied/materialized/removed counts plus a `close`
+  state of `refreshed`, `current`, or `not-required`. Package build remains a
+  separate pipeline step; existing package outputs are reported stale.
+
+This policy never auto-promotes architecture, business, decision, test, or
+other semantic knowledge. Agents must not infer a human gate from a phase-local
+result. Human gates and their inspection/resolution Actions are exposed only by
+`workflow.current`.
+
+Approved codegraph sections use the local evidence form
+`src-N#symbol:<file>:<symbol>:<kind>@<digest>`. The file segment makes reverse
+lookup exact when multiple files contain the same symbol name, kind, and digest;
+the complete ref remains opaque to agents. New pages keep only top-level
+`candidate_fingerprint` and do not emit `code_origin`.
+
+### `extractCustom`
+
+Use a project-owned extractor when code facts cannot be represented by the
+TypeScript symbol extractor, for example a language-specific parser or an
+aggregated repository protocol:
+
+```ts
+extractCustom({
+  id: "extract:service:protocol",
+  sources: [service],
+  collection: "codegraph",
+  extract: async ({ projectRoot }) => ({
+    candidates: [{
+      nodeRef: "service/protocol",
+      kind: "protocol",
+      visibility: "exported",
+      module: "service",
+      markdown: renderProtocol(projectRoot),
+      evidence: [{
+        source: "20260811/service",
+        file: "src/protocol.ts",
+        symbol: "protocol",
+        kind: "variable",
+        digest: "0123456789ab",
+      }],
+      review: {
+        title: "Service protocol",
+        summary: "Aggregated protocol boundary.",
+        signals: ["source-backed"],
+        reason: "Review the project-owned extraction.",
+      },
+    }],
+  }),
+});
+```
+
+`sources` is the complete registered repo scope for the phase. Every candidate
+and edge carries structured `evidence`; the CLI validates that evidence against
+the declared sources, creates canonical `source_ref` values, writes the symbol
+index, candidate ledger and Review snapshots atomically, and records a phase
+fingerprint. `context status` therefore treats this phase exactly like another
+pending code extraction target, and Review can verify snapshot freshness
+without a placeholder `extractTs` phase.
+
+The extractor returns knowledge semantics (`nodeRef`, rendered Markdown,
+Review summary and source-backed evidence). It must not write `knowledge/`,
+`.tmp/context-runtime/lifecycle/candidates.jsonl`, extraction fingerprints or
+Review snapshots directly. Context owns those files and preserves rejected and
+unchanged-approved decisions across reruns.
+
+### `reviewValidity`
+
+Declare the review step for a collection:
+
+```ts
+reviewValidity({ collection: "codegraph" });
+```
+
+Declare one review gate for all current draft collections:
+
+```ts
+reviewValidity({ scope: "all" });
+```
+
+Phase id:
+
+```text
+review:codegraph:validity
+review:all:validity
+```
+
+The review HTML and apply flow are CLI-owned.
+
+This phase marks a human review gate when current candidates exist. Agents
+should run `context review html <collection> --open --format json` or `context
+review html --all --open --format json`, confirm the returned `opened` field,
+and wait for the user-copied payload. They should not run the phase as an
+automatic approval step or synthesize a payload themselves.
+
+The only batch-wide exception is explicit current-conversation fully managed
+authority. In that mode, follow the `context status --managed` route to
+`context review approve-all ... --managed`; the CLI validates the exact current
+scope before applying one default-approved decision.
+
+The gate is batch-scoped: prose waits for every planned View across all active
+structure slots and every declared `pendingStructureTargets` item in the round;
+codegraph waits for every pending extract phase in the confirmed module round.
+Candidate count/hash therefore describes the complete current batch rather than
+one page, source slot, or module. Deterministic close later merges all active
+slots into `knowledge/structure.yaml`, retains only their source, collection,
+and consumed snapshot hash as `source_inputs`, then removes the lifecycle slots.
+
+`status.structureBatch` lists unclassified, configuration-required, pending,
+and active structure slots together with the execution policy for the round.
+
+If the user explicitly asks for an automated or quick approval/rejection path,
+use the scoped quick commands instead of hand-writing a payload:
+
+```bash
+context review approve <candidate-id> --collection <collection>
+context review reject <candidate-id> --all
+```
+
+These commands still compute the current review scope and apply the same
+candidate-id gate as the copied payload flow. They are not a replacement for the
+default human review gate.
+
+### `customPhase`
+
+Use only when the typed factories cannot express a project-specific workflow:
+
+```ts
+const sample = source("20260712", "sample");
+
+customPhase("custom:20260712/sample:review", async (ctx) => {
+  await ctx.ensureSources({ source: sample });
+  await ctx.extract.ts(extractTs({ source: sample, collection: "codegraph" }));
+  await ctx.review.html(reviewValidity({ collection: "codegraph" }));
+});
+```
+
+Custom phases are an orchestration escape hatch. Use `extractCustom()` instead
+when project code needs to publish codegraph candidates. The supported runtime
+helpers are:
+
+- `ctx.ensureSources(...)` for repo source readiness.
+- `ctx.extract.ts(...)` for declared TypeScript extraction.
+- `ctx.review.html(...)` for the human review HTML gate.