@documentation-robotics/cli 0.2.0 → 0.4.0

package/dist/mcp/tools/codebase-extract.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../../src/mcp/tools/codebase-extract.ts"],
+  "sourcesContent": ["/**\n * codebase_extract \u2014 run the extraction cascade over the indexed code and stage what it finds in\n * an as-built changeset. It never writes the base model and never commits.\n *\n * The cascade (docs/analyzers/CASCADE_DESIGN.md):\n * 1. Tier 0 rules decide what they can; a CBM route is an `api.operation` by the node mapping.\n *    Those decisions are staged, with the relationships the edge mapping gives them.\n * 2. Tier 1 (a decision model) is not wired until the per-project opt-in is settled\n *    (docs/EXTRACTION_STRATEGY.md, B6); it would decide cards between steps 1 and 3.\n * 3. The calling agent gets the rest as cards, paged, and stages its own decisions with model_add.\n *\n * Only what differs from the model is staged (src/analyzers/extraction-plan.ts): existing elements\n * are matched by source file and symbol; a changed match is an update, no match is an add, and an\n * element whose code is gone is listed as a candidate delete, never staged. Re-running on unchanged\n * code stages nothing. `since` limits the run to files changed since a git ref, which is how the\n * verify workflow extracts a branch's build for changeset_verify.\n *\n * It runs inline: on this repository (4,800 cards, 25,000 mapped edges) a run takes a few seconds.\n * The extraction changeset is active afterwards, so the agent's model_add calls stage into it;\n * the one active before is returned as previousActive. A run that stages nothing creates and\n * activates no changeset: its cards wait in pending.json for the changeset the agent creates.\n *\n * \"Not an element\" decisions are kept per project (.dr/analyzers/extract/decisions.json), by file\n * and symbol: a card or staged symbol the agent rejects (`reject`, which unstages what is still\n * staged for it), and an element this tool staged that the agent then unstaged. Later runs leave\n * those symbols out, and say how many; `clearRejected` forgets them.\n */\n\nimport { existsSync, readFileSync } from \"node:fs\";\nimport { mkdir, readFile, readdir, rm, writeFile } from \"node:fs/promises\";\nimport path from \"node:path\";\nimport { z } from \"zod\";\nimport { strictItem } from \"../strict-schema.js\";\nimport type { CallToolResult } from \"@modelcontextprotocol/sdk/types.js\";\nimport { codeChangesSince, inDirs, scopeChanges, type CodeChangesResult } from \"../../analyzers/code-changes.js\";\nimport { SOURCE_EXT, VENDOR_EXCLUDE } from \"../../analyzers/cards/build.js\";\nimport { ExtractionTimeoutError, type ExtractionGraph } from \"../../analyzers/cards/extract.js\";\nimport {\n  attributeChangedLines,\n  decisionKey,\n  needsAttributesCard,\n  planElements,\n  planRelationships,\n  sortUndecided,\n  sourceSymbolOf,\n  type ElementPlan,\n  type PlannedElement,\n  type PlannedRelationship,\n  type PlannedUpdate,\n  type UndecidedCard,\n  type UndecidedKind,\n} from \"../../analyzers/extraction-plan.js\";\nimport { Changeset, type StagedChange } from \"../../core/changeset.js\";\nimport { ChangesetGraph } from \"../../core/changeset-graph.js\";\nimport { Element } from \"../../core/element.js\";\nimport { Layer } from \"../../core/layer.js\";\nimport type { Model } from \"../../core/model.js\";\nimport { setStagedSourceReference, stagedSourceReference } from \"../../core/staged-source-reference.js\";\nimport { StagingAreaManager } from \"../../core/staging-area.js\";\nimport { getAllLayerIds, isValidLayer } from \"../../generated/layer-registry.js\";\nimport { getValidRelationships } from \"../../generated/relationship-index.js\";\nimport type { SourceReference } from \"../../types/source-reference.js\";\nimport { generateUUID } from \"../../utils/id-generator.js\";\nimport { CLIError, ErrorCategory, formatValidOptions } from \"../../utils/errors.js\";\nimport { FileLock } from \"../../utils/file-lock.js\";\nimport { SchemaValidator } from \"../../validators/schema-validator.js\";\nimport { compactJson, jsonResult, loadModel, reloadModel, rootPathSchema, runTool, type McpToolContext, type McpToolDefinition } from \"./shared.js\";\nimport { changesetUnstageHandler } from \"./changeset-editing.js\";\nimport {\n  analyzerNotFoundError,\n  canonicalRoots,\n  defaultCodebaseToolDeps,\n  describeIndex,\n  requireFreshIndex,\n  type CodebaseToolDeps,\n} from \"./codebase-shared.js\";\n\nconst DEFAULT_PAGE_SIZE = 25;\n/** The most cards a page holds, whatever pageSize asks: more than this rarely fits the response budget. */\nconst MAX_PAGE_SIZE = 50;\n/**\n * The size a response with cards aims to stay under. Clients save larger tool results to a file\n * (Claude Code does above about 25-30 KB), which the agent then has to search.\n */\nconst RESPONSE_BUDGET_BYTES = 28 * 1024;\nconst MAX_LISTED = 100;\n\nconst inputSchema = {\n  changeset: z\n    .string()\n    .min(1)\n    .optional()\n    .describe(\n      \"Name (or id) of the as-built changeset to stage into. Created when absent, reused when it is staged. \" +\n        \"Default: extract-<short git HEAD>, or extract-<since base>..<HEAD> with since.\"\n    ),\n  since: z\n    .string()\n    .min(1)\n    .optional()\n    .describe(\n      \"A git ref (branch, tag or commit). Extract only the files changed since its merge base with HEAD, plus \" +\n        \"uncommitted ones. To verify a branch's build, pass the branch it started from.\"\n    ),\n  layers: z.array(z.string()).optional().describe(\"Only these layers (canonical names). Default: every layer.\"),\n  pageSize: z\n    .number()\n    .int()\n    .min(1)\n    .max(200)\n    .optional()\n    .describe(\n      `Undecided cards per page (default ${DEFAULT_PAGE_SIZE}, at most ${MAX_PAGE_SIZE}). A page that would make the response larger than about ` +\n        `${RESPONSE_BUDGET_BYTES / 1024} KB has its cards shortened, and says so.`\n    ),\n  page: z\n    .number()\n    .int()\n    .min(1)\n    .optional()\n    .describe(\n      \"Page of undecided cards (default 1). Page 2 and later read the last run's cards, with its since and layers: nothing is extracted or staged.\"\n    ),\n  reject: z\n    .array(\n      strictItem(\"A reject[] item\", {\n        card: z\n          .string()\n          .min(1)\n          .describe(\"The card's cardId, its symbol (or file#symbol), or the id of an element this extraction staged.\"),\n        reason: z.string().min(1).describe(\"Why it is not a model element, in a few words.\"),\n      })\n    )\n    .optional()\n    .describe(\n      \"Code that is not a model element: a card of this extraction (cardId, or a symbol only one card has), a symbol it \" +\n        \"staged (Tier 0 decided it), or the id of an element staged from it. Recorded for the project until cleared, so \" +\n        \"later runs leave them out; an element still staged in the changeset for it is unstaged, with its relationships. \" +\n        \"A call with only reject or clearRejected records and runs nothing.\"\n    ),\n  clearRejected: z\n    .union([z.literal(true), z.array(z.string().min(1))])\n    .optional()\n    .describe(\"Forget not-an-element decisions: true for all, or a list of symbols (or file#symbol) as notElements lists them.\"),\n  rootPath: rootPathSchema,\n};\n\nexport type CodebaseExtractArgs = z.infer<z.ZodObject<typeof inputSchema>>;\n\n/**\n * The last run on a changeset: its undecided cards, for paging, the arguments and model they came\n * from, and the changeset that was active before the first run.\n */\ninterface StoredCards {\n  changesetId: string;\n  changesetName: string;\n  gitHead: string;\n  since: string | null;\n  layers: string[] | null;\n  /** The base model's manifest timestamp when the cards were read. */\n  baseModified?: string;\n  previousActive?: { id: string; name: string } | null;\n  createdAt: string;\n  cards: UndecidedCard[];\n  /** The elements extraction staged into this changeset, by the symbol they came from. */\n  staged?: StagedBySymbol[];\n  /**\n   * Cards earlier runs returned that are no longer undecided (the agent modelled them), so a\n   * `reject` can still name them by cardId, e.g. after unstaging the element it added for one.\n   */\n  earlierCards?: EarlierCard[];\n  /**\n   * A run that staged nothing and so made no changeset (`changesetId` is empty): its cards, kept\n   * in {@link PENDING_FILE} for paging and `reject`, and adopted by the changeset of that name\n   * once it exists.\n   */\n  pending?: true;\n  /**\n   * Updates extraction itself staged into this changeset, with the fields it changed (an update\n   * folded into an add this changeset stages included), accumulated across runs. An entry goes\n   * when its change is unstaged or the element is rejected.\n   */\n  updated?: Array<{\n    id: string;\n    fields: string[];\n    /**\n     * The value extraction wrote for each field, keyed as in `fields`: a top-level field by its\n     * on-disk name (`description`, `name`, `source_reference`), an attribute as\n     * `attributes.<key>` (`attributes.http_path`). The latest run's value wins.\n     */\n    values?: Record<string, unknown>;\n  }>;\n  /** Ids extraction listed as candidate deletes for this changeset, accumulated across runs. */\n  candidateDeletes?: string[];\n}\n\n/** A card of an earlier run, as the card was (older records kept only the identifying fields). */\ntype EarlierCard = Pick<UndecidedCard, \"cardId\" | \"file\" | \"symbol\" | \"label\" | \"qualifiedName\"> & Partial<UndecidedCard>;\n\ninterface StagedBySymbol {\n  id: string;\n  file: string | null;\n  symbol: string;\n  label: string;\n  /** The element name it was staged with. */\n  name?: string;\n  /** The attributes it was staged with, when it had any. */\n  attributes?: Record<string, unknown>;\n}\n\n/** An element's name and attributes for its {@link StagedBySymbol} entry. */\nfunction stagedAs(name: string | undefined, attributes: Record<string, unknown> | undefined): Pick<StagedBySymbol, \"name\" | \"attributes\"> {\n  return { ...(name ? { name } : {}), ...(attributes && Object.keys(attributes).length ? { attributes: structuredClone(attributes) } : {}) };\n}\n\n/** Descriptions extraction wrote from docstrings, by element id (see PlanOptions.extractedDescriptions). */\nconst DESCRIPTIONS_FILE = \"descriptions.json\";\n\n/** \"Not an element\" decisions, by {@link decisionKey}. */\nconst DECISIONS_FILE = \"decisions.json\";\n\ninterface NotElementDecision {\n  file: string | null;\n  symbol: string;\n  label?: string;\n  reason: string;\n  /** `rejected`: the agent passed it in `reject`. `unstaged`: extraction staged it and it was unstaged. */\n  how: \"rejected\" | \"unstaged\";\n  changeset: string;\n  /**\n   * The changeset it came from. An `unstaged` decision lasts only while that changeset is staged\n   * (discarding or landing it drops the decision); a `rejected` one lasts until cleared.\n   */\n  changesetId?: string;\n  at: string;\n}\n\ninterface DecisionsFile {\n  version: 1;\n  notElements: Record<string, NotElementDecision>;\n}\n\n/** The cards of the last run that staged nothing, so made no changeset ({@link StoredCards.pending}). */\nconst PENDING_FILE = \"pending.json\";\n\nconst KEEP_FILES = new Set([DESCRIPTIONS_FILE, DECISIONS_FILE, PENDING_FILE]);\n\nfunction extractDir(projectRoot: string): string {\n  return path.join(projectRoot, \".dr\", \"analyzers\", \"extract\");\n}\n\nfunction cardsPath(projectRoot: string, changesetId: string): string {\n  return path.join(extractDir(projectRoot), `${changesetId.replace(/[^\\w.-]/g, \"_\")}.json`);\n}\n\n/**\n * Whether a changeset is one codebase_extract stages into: it has the extraction's record (its\n * cards file, which a run or a reject writes, adopted waiting cards included), or, given its name,\n * it is the changeset the waiting cards of a run that staged nothing name.\n */\nexport async function isExtractionChangeset(projectRoot: string, changesetId: string, changesetName?: string): Promise<boolean> {\n  const stored = await readJson<StoredCards>(cardsPath(projectRoot, changesetId));\n  if (stored && !stored.pending && stored.changesetId === changesetId) return true;\n  if (!changesetName) return false;\n  const pending = await readJson<StoredCards>(path.join(extractDir(projectRoot), PENDING_FILE));\n  return !!pending?.pending && pending.changesetName === changesetName;\n}\n\n/** A catalog check by triple id (`layer.type.predicate.layer.type`). */\nfunction hasTriple(id: string): boolean {\n  const parts = id.split(\".\");\n  if (parts.length !== 5) return false;\n  return getValidRelationships(`${parts[0]}.${parts[1]}`, parts[2], `${parts[3]}.${parts[4]}`).length > 0;\n}\n\nfunction emptyChangeset(): Changeset {\n  const now = new Date().toISOString();\n  return new Changeset({ id: \"extract-preview\", name: \"extract\", created: now, modified: now, status: \"staged\", baseSnapshot: \"\", changes: [] });\n}\n\nfunction page<T>(items: T[], pageNumber: number, pageSize: number) {\n  const pages = Math.ceil(items.length / pageSize);\n  return {\n    total: items.length,\n    page: pageNumber,\n    pageSize,\n    pages,\n    items: items.slice((pageNumber - 1) * pageSize, pageNumber * pageSize),\n  };\n}\n\nfunction capped<T>(items: T[], limit = MAX_LISTED): { total: number; items: T[]; truncated?: true } {\n  return items.length > limit ? { total: items.length, items: items.slice(0, limit), truncated: true } : { total: items.length, items };\n}\n\n/** How much of each card a page shows: all of it, shortened, or only what deciding needs. */\ntype CardDetail = \"full\" | \"shortened\" | \"compact\";\n\n/** Kinds whose reason is the same sentence on every card of the kind. */\nconst GENERIC_REASON: ReadonlySet<UndecidedKind> = new Set([\"no-rule\", \"narrowed\"]);\n\nfunction clip(text: string | undefined, max: number): string | undefined {\n  if (!text) return text;\n  return text.length > max ? `${text.slice(0, max - 3)}...` : text;\n}\n\nfunction cardAt<T extends UndecidedCard>(card: T, detail: CardDetail): Partial<T> {\n  if (detail === \"full\") return card;\n  const { reason, docstring, signature, decorators, candidates, qualifiedName, ...rest } = card;\n  const open = candidates.length ? { candidates } : {};\n  if (detail === \"shortened\") {\n    return {\n      ...rest,\n      qualifiedName,\n      ...open,\n      ...(signature ? { signature: clip(signature, 80) } : {}),\n      ...(docstring ? { docstring: clip(docstring, 120) } : {}),\n      ...(decorators ? { decorators } : {}),\n      ...(GENERIC_REASON.has(card.kind) ? {} : { reason }),\n    } as Partial<T>;\n  }\n  return { ...rest, ...open, ...(card.kind === \"ambiguous\" || card.kind === \"needs-attributes\" ? { reason: clip(reason, 200) } : {}) } as Partial<T>;\n}\n\nconst PAGE_NOTES: Record<Exclude<CardDetail, \"full\">, string> = {\n  shortened:\n    \"Docstrings and signatures are shortened, and empty candidates and reasons that only name the card's kind left out, to keep this response small.\",\n  compact: \"Docstrings, signatures, decorators, qualified names, empty candidates and most reasons are left out, to keep this response small.\",\n};\n\n/** How a response was fitted under the budget. */\ninterface PageFit {\n  /** The cards' detail, when less than full, with a note saying what was left out. */\n  detail?: Exclude<CardDetail, \"full\">;\n  note?: string;\n  /** The page was cut to its first `shown` cards; `readOn` says how to read the ones after. */\n  shown?: number;\n  readOn?: string;\n  /** The lists other than the cards (candidate deletes, updates, retyped, recorded decisions) show at most this many items. */\n  listLimit?: number;\n  /** Nothing fitted: even this, the smallest response, is over the budget. */\n  overBudget?: true;\n}\n\ntype CardPage = ReturnType<typeof page<UndecidedCard>>;\n\n/** How many items the other lists show, largest first, when they alone would fill the budget. */\nconst LIST_LIMITS = [MAX_LISTED, 20, 5, 0];\n\n/** The paging call that continues after a page cut to its first `shown` cards. */\nfunction cutInstruction(p: CardPage, shown: number): string {\n  const next = (p.page - 1) * p.pageSize + shown;\n  return (\n    `call codebase_extract with page: ${Math.floor(next / shown) + 1} and pageSize: ${shown}` +\n    `${next % shown ? \" (its first cards may repeat ones you have)\" : \"\"}`\n  );\n}\n\n/**\n * The response with a page of cards, at the most detail that keeps it under the budget. The other\n * lists come first: when they alone would fill it, they are shortened (`listLimit`). Then the\n * cards: shortened, then compact, then the page cut short (`shown`, with `readOn`). When even one\n * compact card and empty lists don't fit, the smallest response is returned with `overBudget`.\n * `render` builds the whole response from the page's cards and how it fitted them.\n */\nfunction fitCards(cards: UndecidedCard[], p: CardPage, render: (items: Array<Partial<UndecidedCard>>, fit: PageFit) => Record<string, unknown>): Record<string, unknown> {\n  const fits = (result: Record<string, unknown>) => Buffer.byteLength(compactJson(result), \"utf-8\") <= RESPONSE_BUDGET_BYTES;\n  let lists: PageFit = {};\n  let listsFit = false;\n  for (const limit of LIST_LIMITS) {\n    lists = limit < MAX_LISTED ? { listLimit: limit } : {};\n    if (fits(render([], lists))) {\n      listsFit = true;\n      break;\n    }\n  }\n  const compact = cards.map((c) => cardAt(c, \"compact\"));\n  const smallest = (): Record<string, unknown> =>\n    render(compact.slice(0, 1), {\n      ...lists,\n      ...(cards.length ? { detail: \"compact\", note: PAGE_NOTES.compact } : {}),\n      ...(cards.length > 1 ? { shown: 1, readOn: cutInstruction(p, 1) } : {}),\n      overBudget: true,\n    });\n  if (!listsFit) return smallest();\n  let result = render(cards, lists);\n  if (fits(result)) return result;\n  for (const detail of [\"shortened\", \"compact\"] as const) {\n    result = render(\n      cards.map((c) => cardAt(c, detail)),\n      { ...lists, detail, note: PAGE_NOTES[detail] }\n    );\n    if (fits(result)) return result;\n  }\n  for (let shown = compact.length - 1; shown >= 1; shown--) {\n    result = render(compact.slice(0, shown), { ...lists, detail: \"compact\", note: PAGE_NOTES.compact, shown, readOn: cutInstruction(p, shown) });\n    if (fits(result)) return result;\n  }\n  return smallest();\n}\n\n/** The response's notes on what fitting it left out, at its top level. */\nfunction fitNotes(fit: PageFit): Record<string, unknown> {\n  return {\n    ...(fit.listLimit !== undefined\n      ? {\n          listsShortened:\n            `candidateDeletes, staged.updated, retyped and notElements.recorded list at most ${fit.listLimit} item(s) here, to keep the response small; ` +\n            \"each total is the full count. Narrow the run with layers or since to list the rest.\",\n        }\n      : {}),\n    ...(fit.overBudget ? { overBudget: `Even shortened, this response is over about ${RESPONSE_BUDGET_BYTES / 1024} KB.` } : {}),\n  };\n}\n\n/** The undecided section of a response: the page, how it was fitted, and how to read on. */\nfunction undecidedSection(p: CardPage, items: Array<Partial<UndecidedCard>>, fit: PageFit, requestedPageSize: number, extra: Record<string, unknown> = {}): Record<string, unknown> {\n  return {\n    ...p,\n    items,\n    ...extra,\n    ...(requestedPageSize > p.pageSize ? { pageSizeCapped: `pageSize ${requestedPageSize} was capped at ${p.pageSize}; use page: 2 and on for more.` } : {}),\n    ...(fit.detail ? { detail: fit.detail, detailNote: `${fit.note} A smaller pageSize gives full cards.` } : {}),\n    ...(fit.shown !== undefined\n      ? { cut: `This page was cut to its first ${fit.shown} of ${p.items.length} cards to keep the response small. For the rest, ${fit.readOn}.` }\n      : {}),\n  };\n}\n\n// ---------------------------------------------------------------------------\n// Staging\n// ---------------------------------------------------------------------------\n\nfunction elementOfAdd(add: PlannedElement, now: string): Element {\n  const element = new Element({\n    id: generateUUID(),\n    path: add.id,\n    spec_node_id: `${add.layer}.${add.type}`,\n    layer_id: add.layer,\n    type: add.type,\n    name: add.name,\n    description: add.description,\n    attributes: add.attributes,\n    metadata: { created_at: now, updated_at: now, version: 1 },\n    layer: add.layer,\n  });\n  if (add.sourceReference) element.setSourceReference(add.sourceReference);\n  return element;\n}\n\n/** Adds whose attributes validate, and the rest as cards with what they lack. */\nasync function validateAdds(adds: PlannedElement[], project: string, now: string, hunks?: CodeChangesResult[\"hunks\"]) {\n  const valid: Array<{ add: PlannedElement; element: Element }> = [];\n  const invalid: UndecidedCard[] = [];\n  const validator = new SchemaValidator();\n  const byLayer = new Map<string, Array<{ add: PlannedElement; element: Element }>>();\n  for (const add of adds) {\n    const list = byLayer.get(add.layer) ?? byLayer.set(add.layer, []).get(add.layer)!;\n    list.push({ add, element: elementOfAdd(add, now) });\n  }\n  for (const [layerName, items] of byLayer) {\n    const layer = new Layer(layerName);\n    for (const item of items) layer.addElement(item.element);\n    const result = await validator.validateLayer(layer);\n    const errors = new Map<string, string[]>();\n    for (const e of result.errors) {\n      if (!e.elementId) continue;\n      (errors.get(e.elementId) ?? errors.set(e.elementId, []).get(e.elementId)!).push(e.message);\n    }\n    for (const item of items) {\n      const errs = errors.get(item.add.id);\n      if (errs?.length) invalid.push(needsAttributesCard(item.add, project, errs, hunks));\n      else valid.push(item);\n    }\n  }\n  return { valid, invalid };\n}\n\n/** The element as the changeset currently has it, in the on-disk shape. */\nasync function currentSnapshot(model: Model, graph: ChangesetGraph, changeset: Changeset, id: string, layer: string) {\n  const element = graph.getElement(id);\n  if (element && element.status !== \"unchanged\") {\n    const changes = (changeset.changes as StagedChange[]).filter(\n      (c) => (c.type === \"add\" || c.type === \"update\") && c.after && graph.resolve(c.elementId) === id\n    );\n    const last = changes[changes.length - 1];\n    if (last?.after) return { snapshot: structuredClone(last.after), stagedAdd: element.status === \"added\" ? changes.find((c) => c.type === \"add\") : undefined };\n  }\n  const base = (await model.getBaseLayer(layer))?.getElement(id);\n  return base ? { snapshot: structuredClone(base.toJSON() as unknown as Record<string, unknown>), stagedAdd: undefined } : null;\n}\n\nfunction patched(snapshot: Record<string, unknown>, update: PlannedUpdate, now: string): Record<string, unknown> {\n  const after = structuredClone(snapshot);\n  for (const [field, value] of Object.entries(update.fields)) {\n    if (field === \"source_reference\") setStagedSourceReference(after, value as SourceReference);\n    else if (field.startsWith(\"attributes.\")) {\n      after.attributes = { ...((after.attributes as Record<string, unknown>) ?? {}), [field.slice(\"attributes.\".length)]: value };\n    } else after[field] = value;\n  }\n  const metadata = after.metadata as Record<string, unknown> | undefined;\n  if (metadata) after.metadata = { ...metadata, updated_at: now };\n  return after;\n}\n\nfunction relationshipChange(r: PlannedRelationship): Omit<StagedChange, \"sequenceNumber\"> {\n  return {\n    type: \"relationship-add\",\n    elementId: `${r.source}::${r.predicate}::${r.target}`,\n    layerName: r.sourceLayer,\n    after: {\n      source: r.source,\n      target: r.target,\n      predicate: r.predicate,\n      layer: r.sourceLayer,\n      ...(r.targetLayer !== r.sourceLayer ? { targetLayer: r.targetLayer } : {}),\n      category: \"structural\",\n    },\n  };\n}\n\n// ---------------------------------------------------------------------------\n// Result\n// ---------------------------------------------------------------------------\n\nfunction byLayer(adds: PlannedElement[], updates: PlannedUpdate[], relationships: PlannedRelationship[]) {\n  const out: Record<string, { adds: number; updates: number; relationships: number }> = {};\n  const at = (layer: string) => (out[layer] ??= { adds: 0, updates: 0, relationships: 0 });\n  for (const a of adds) at(a.layer).adds++;\n  for (const u of updates) at(u.layer).updates++;\n  for (const r of relationships) at(r.sourceLayer).relationships++;\n  return Object.fromEntries(Object.entries(out).sort(([a], [b]) => a.localeCompare(b)));\n}\n\nfunction notElementsResult(\n  decisions: DecisionsFile,\n  skipped: number,\n  recorded: Array<{ symbol: string; file: string | null; how: NotElementDecision[\"how\"] }>,\n  cleared: number,\n  listLimit = MAX_LISTED\n) {\n  const total = Object.keys(decisions.notElements).length;\n  if (!total && !skipped && !recorded.length && !cleared) return {};\n  return {\n    notElements: {\n      total,\n      skipped,\n      ...(recorded.length ? { recorded: capped(recorded, listLimit) } : {}),\n      ...(cleared ? { cleared } : {}),\n      note: \"Symbols decided not to be elements (rejected, or unstaged after this tool staged them). Runs leave them out; clearRejected forgets them.\",\n    },\n  };\n}\n\n/** Verify mode, the card step: stage cards as the code names them, never as the plan does. */\nfunction verifyCardStep(undecidedPages: number, readOn?: string): string {\n  return (\n    \"Stage the element cards with model_add, named after the card's symbol (the card's name when it has one), never the plan's element, and never copy plan elements here: \" +\n    'a layer and type from its candidates or hint, sourceFile = file, sourceSymbol = symbol, sourceProvenance: \"extracted\". ' +\n    `Ask the user about cards you can't place, in one short list. ${readFurther(undecidedPages, readOn)}`\n  );\n}\n\n/** Verify mode, after verify: the plan lands, not the as-built changeset. */\nfunction verifyLandStep(plan: { id: string; name: string }, why = \"\"): string {\n  return (\n    `After verify, the plan '${plan.name}' lands (changeset_commit when the user asks), not this changeset: discard this one or keep it as a record. ` +\n    `Landing it first drifts the plan's base, so the plan would need force. Call changeset_activate with \"${plan.id}\" to resume the plan${why}.`\n  );\n}\n\n/**\n * Verify mode with nothing to stage or decide: no as-built changeset exists, so the plan is\n * verified against the model, with extraction's blind spots applied.\n */\nfunction verifyNothingSteps(plan: { id: string; name: string }, since: string): string[] {\n  return [\n    `Nothing in the range since ${since} is observable to extraction or differs from the model, so no as-built changeset was created: there is none to verify against. '${plan.name}' is still active.`,\n    `Call changeset_verify with planned: \"${plan.id}\" and against: {base: true, extracted: true}: it compares the plan with the model, and what extraction can't see is unverifiable rather than missing.`,\n  ];\n}\n\n/** How to read the cards after this page: the cut's paging call when the page was cut. */\nfunction readFurther(undecidedPages: number, readOn?: string): string {\n  return readOn\n    ? `This page was cut to keep the response small: for the cards after it, ${readOn}, and page on with that pageSize.`\n    : `Read further pages with page: 2 and on (${undecidedPages} in all).`;\n}\n\nfunction nextSteps(\n  changeset: { id: string; name: string },\n  previous: { id: string; name: string } | null,\n  undecidedPages: number,\n  plan: Pick<ElementPlan, \"candidateDeletes\" | \"retyped\">,\n  changedCards = 0,\n  since?: string,\n  readOn?: string\n): string[] {\n  const steps = [\n    `The as-built changeset '${changeset.name}' is active: model_add, model_update, model_delete and relationship_add stage into it. Nothing reaches the base model until the user lands it.`,\n  ];\n  if (changedCards > 0) {\n    steps.push(\n      `${changedCards} card(s) have changedInRange: their lines are new or changed in the range, so they come first. The rest are symbols in the same files that the range didn't touch.`\n    );\n  }\n  // A since run with a plan active before it is the verify workflow: this changeset is the\n  // as-built side the plan is checked against, not a change to land.\n  const verify = !!since && !!previous;\n  const rerun = `codebase_extract again with changeset: \"${changeset.name}\"${since ? `, since: \"${since}\"` : \"\"}`;\n  if (undecidedPages > 0) {\n    steps.push(\n      verify\n        ? verifyCardStep(undecidedPages, readOn)\n        : \"Decide the undecided cards: for each one that is a model element, call model_add with a layer and type from its candidates \" +\n            \"(or its hint; spec_type says what a type needs), a name (the card's name when it has one), sourceFile = file, sourceSymbol = symbol and sourceProvenance: \\\"extracted\\\". \" +\n            readFurther(undecidedPages, readOn),\n      \"For cards that are not elements, call codebase_extract with reject: [{card: cardId, reason}] so later runs leave them out.\",\n      verify\n        ? `Call ${rerun} for their relationships.`\n        : `Then call ${rerun} (it keeps that run's since and layers). It finds your elements by their source reference and stages the relationships the edge mapping gives them.`\n    );\n  }\n  if (plan.candidateDeletes.length) {\n    steps.push(\n      \"Check candidateDeletes: call model_delete only for elements whose code is really gone (replacedBy names the element staged for a renamed file). \" +\n        \"reference-never-matched means the element's reference was wrong before the range: the range removed nothing, so fix or delete the element without blaming the range.\"\n    );\n  }\n  if (plan.retyped.length) {\n    steps.push(\"retyped lists elements whose type the rules now decide differently. Leave them unless the rule is right; changing a type means adding the new element and deleting the old.\");\n  }\n  if (verify) {\n    steps.push(\n      `Then call changeset_verify with planned: \"${previous!.id}\" and against: {changesetId: \"${changeset.id}\"}.`,\n      verifyLandStep(previous!)\n    );\n    return steps;\n  }\n  steps.push(\"Call changeset_brief to see what the changeset covers and its gaps, then review_open and give the user the link.\");\n  if (previous) {\n    steps.push(\n      `'${previous.name}' was active before this call. To check it against this build, call changeset_verify with planned: \"${previous.id}\" and against: {changesetId: \"${changeset.id}\"}. Call changeset_activate with \"${previous.id}\" to resume it.`\n    );\n  } else {\n    steps.push(\"The user lands the changeset with changeset_commit (they confirm in a dialog) or in the viewer.\");\n  }\n  return steps;\n}\n\n/**\n * Next steps for a run that staged nothing but left cards or candidate deletes: no changeset was\n * made, so the agent makes one before staging anything for them.\n */\nfunction pendingSteps(\n  name: string,\n  active: { id: string; name: string } | null,\n  undecidedPages: number,\n  plan: Pick<ElementPlan, \"candidateDeletes\">,\n  changedCards: number,\n  since?: string,\n  readOn?: string\n): string[] {\n  // A since run with a plan active is the verify workflow: the changeset to create is the\n  // as-built side, and creating it deactivates the plan.\n  const verify = !!since && !!active;\n  const steps = [\n    verify\n      ? `Nothing was staged, so no as-built changeset was created and '${active!.name}' is still active. Before you stage a card or delete a candidate, call changeset_create with name: \"${name}\" ` +\n        `(it becomes active, so model_add and model_delete stage into it and not into the plan).`\n      : `Nothing was staged, so no changeset was created or activated. Before you model a card or delete a candidate, call changeset_create with name: \"${name}\" ` +\n        `(it becomes active, and model_add and model_delete stage into it); without it they would ${active ? `stage into '${active.name}'` : \"write the base model\"}.`,\n  ];\n  if (changedCards > 0) {\n    steps.push(`${changedCards} card(s) have changedInRange: their lines are new or changed in the range, so they come first. The rest are symbols in the same files that the range didn't touch.`);\n  }\n  if (undecidedPages > 0) {\n    steps.push(\n      verify\n        ? verifyCardStep(undecidedPages, readOn)\n        : \"For each card that is a model element, call model_add (into that changeset) with a layer and type from its candidates (or its hint), a name (the card's name when it has one), \" +\n            `sourceFile = file, sourceSymbol = symbol and sourceProvenance: \"extracted\". ${readFurther(undecidedPages, readOn)}`,\n      \"For cards that are not elements, call codebase_extract with reject: [{card: cardId, reason}] so later runs leave them out; that needs no changeset.\",\n      verify\n        ? `Call codebase_extract again with changeset: \"${name}\", since: \"${since}\" for their relationships.`\n        : `After adding elements, call codebase_extract with changeset: \"${name}\"${since ? `, since: \"${since}\"` : \"\"}: it keeps this run's since and layers, and stages the relationships the edge mapping gives them.`\n    );\n  }\n  if (plan.candidateDeletes.length) {\n    steps.push(\n      \"Check candidateDeletes: call model_delete (into that changeset) only for elements whose code is really gone. \" +\n        \"reference-never-matched means the element's reference was wrong before the range: the range removed nothing.\"\n    );\n  }\n  if (verify) {\n    steps.push(\n      `Then call changeset_verify with planned: \"${active!.id}\" and against: {changesetId: \"${name}\"}.`,\n      verifyLandStep(active!, \" (changeset_create deactivated it)\"),\n      `If no card is an element and nothing is deleted, there is no as-built changeset to verify against: call changeset_verify with planned: \"${active!.id}\" and against: {base: true, extracted: true} instead.`\n    );\n    return steps;\n  }\n  steps.push(\"If none of these need modelling now, there is nothing to land and nothing to clean up.\");\n  return steps;\n}\n\n// ---------------------------------------------------------------------------\n// Handler\n// ---------------------------------------------------------------------------\n\nconst DEFAULT_BUDGET_MS = 100_000;\nconst NARROW = \"Narrow the run with layers, or with since (a git ref), and call codebase_extract again\";\n\nfunction sameLayers(a: string[] | null, b: string[] | null): boolean {\n  return JSON.stringify([...(a ?? [])].sort()) === JSON.stringify([...(b ?? [])].sort());\n}\n\nasync function readJson<T>(file: string): Promise<T | null> {\n  try {\n    return JSON.parse(await readFile(file, \"utf-8\")) as T;\n  } catch {\n    return null;\n  }\n}\n\n/** Drop the cards files of changesets that are no longer staged. */\nasync function pruneCardFiles(projectRoot: string, manager: StagingAreaManager): Promise<void> {\n  const dir = extractDir(projectRoot);\n  let entries: string[];\n  try {\n    entries = await readdir(dir);\n  } catch {\n    return;\n  }\n  const staged = new Set((await manager.list()).filter((c) => c.status === \"staged\").map((c) => c.id));\n  for (const entry of entries) {\n    if (!entry.endsWith(\".json\") || KEEP_FILES.has(entry)) continue;\n    const stored = await readJson<StoredCards>(path.join(dir, entry));\n    if (!stored || !staged.has(stored.changesetId)) await rm(path.join(dir, entry), { force: true });\n  }\n}\n\n/** The staged changesets with an extraction run at this commit. */\nasync function runsAt(projectRoot: string, manager: StagingAreaManager, head: string): Promise<Changeset[]> {\n  let entries: string[];\n  try {\n    entries = await readdir(extractDir(projectRoot));\n  } catch {\n    return [];\n  }\n  const out: Changeset[] = [];\n  for (const entry of entries) {\n    if (!entry.endsWith(\".json\") || KEEP_FILES.has(entry)) continue;\n    const stored = await readJson<StoredCards>(path.join(extractDir(projectRoot), entry));\n    if (!stored || stored.pending || stored.gitHead !== head || !stored.changesetId) continue;\n    const changeset = await manager.load(stored.changesetId);\n    if (changeset?.status === \"staged\") out.push(changeset);\n  }\n  return out;\n}\n\nasync function readDecisions(projectRoot: string): Promise<DecisionsFile> {\n  const stored = await readJson<DecisionsFile>(path.join(extractDir(projectRoot), DECISIONS_FILE));\n  return { version: 1, notElements: stored?.notElements && typeof stored.notElements === \"object\" ? stored.notElements : {} };\n}\n\nasync function writeDecisions(projectRoot: string, decisions: DecisionsFile): Promise<void> {\n  await mkdir(extractDir(projectRoot), { recursive: true });\n  await writeFile(path.join(extractDir(projectRoot), DECISIONS_FILE), JSON.stringify(decisions, null, 2), \"utf-8\");\n}\n\n/**\n * A piece of code a `reject` may name: a card of this extraction (this run's or an earlier one's),\n * a symbol it staged, or an element of its changeset that names code (staged now, or unstaged).\n */\ninterface Rejectable {\n  file: string | null;\n  symbol: string;\n  label?: string;\n  cardId?: string;\n  qualifiedName?: string;\n  elementId?: string;\n}\n\nfunction normFile(file: string | null | undefined): string | null {\n  return file ? file.replace(/\\\\/g, \"/\").replace(/^\\.\\//, \"\") : null;\n}\n\n/**\n * The code an extraction changeset's own extracted elements name: its staged adds, and the adds\n * unstaged from it. Only `extracted` provenance: an element someone wrote by hand (a planned one,\n * with a manual reference) is never a rejection target.\n */\nfunction changesetRejectables(changeset: Changeset | null, graph: ChangesetGraph | null): Rejectable[] {\n  const out: Rejectable[] = [];\n  for (const e of graph?.elements.values() ?? []) {\n    if (e.status !== \"added\" || e.sourceReference?.provenance !== \"extracted\") continue;\n    for (const l of e.sourceReference.locations ?? []) {\n      if (l.symbol) out.push({ file: normFile(l.file), symbol: l.symbol, elementId: e.id });\n    }\n  }\n  for (const t of changeset?.unstaged ?? []) {\n    if (t.rewritten || t.change.type !== \"add\") continue;\n    const ref = stagedSourceReference(t.change.after as Record<string, unknown> | undefined);\n    if (ref?.provenance !== \"extracted\") continue;\n    for (const l of ref.locations ?? []) {\n      if (l.symbol) out.push({ file: normFile(l.file), symbol: l.symbol, elementId: t.change.elementId });\n    }\n  }\n  return out;\n}\n\n/**\n * What a `reject` names, one symbol per entry, or a CLIError naming the entries it can't place.\n * An entry may be a cardId (of the last run, or an earlier run's card the agent has modelled\n * since), an element id the extraction staged, or a symbol (bare, file#symbol or qualified name)\n * that only one of those has.\n */\nfunction cardsToReject(\n  stored: StoredCards | null,\n  fromChangeset: Rejectable[],\n  changesetName: string,\n  refs: Array<{ card: string; reason: string }>\n): Array<{ file: string | null; symbol: string; label?: string; reason: string }> {\n  const known: Rejectable[] = [\n    ...(stored?.cards ?? []).map((c) => ({ file: c.file, symbol: c.symbol, label: c.label, cardId: c.cardId, qualifiedName: c.qualifiedName })),\n    ...(stored?.earlierCards ?? []).map((c) => ({ file: c.file, symbol: c.symbol, label: c.label, cardId: c.cardId, qualifiedName: c.qualifiedName })),\n    ...(stored?.staged ?? []).map((s) => ({ file: s.file, symbol: s.symbol, label: s.label, elementId: s.id })),\n    ...fromChangeset,\n  ];\n  if (!known.length) {\n    throw new CLIError(`No cards recorded for '${changesetName}' to reject from`, ErrorCategory.USER, [\n      \"Call codebase_extract first, then pass the cardId (or symbol) of each card that is not an element\",\n    ]);\n  }\n  const found: Array<{ file: string | null; symbol: string; label?: string; reason: string }> = [];\n  const unknown: string[] = [];\n  const ambiguous: string[] = [];\n  // The same symbol can be known several ways (a card, then the element staged for it).\n  const distinctSymbols = (matches: Rejectable[]): Rejectable[] => {\n    const bySymbol = new Map<string, Rejectable>();\n    for (const m of matches) {\n      const key = decisionKey(m.file, m.symbol);\n      const seen = bySymbol.get(key);\n      if (!seen || (!seen.label && m.label)) bySymbol.set(key, m);\n    }\n    return [...bySymbol.values()];\n  };\n  for (const ref of refs) {\n    // An element id names the element: every symbol it names (one per source location).\n    const ofElement = known.filter((k) => k.elementId === ref.card);\n    if (ofElement.length) {\n      for (const d of distinctSymbols(ofElement)) found.push({ file: d.file, symbol: d.symbol, label: d.label, reason: ref.reason });\n      continue;\n    }\n    const byCard = known.filter((k) => k.cardId === ref.card);\n    const matches = byCard.length\n      ? byCard\n      : known.filter((k) => k.symbol === ref.card || `${k.file ?? \"\"}#${k.symbol}` === ref.card || k.qualifiedName === ref.card);\n    const distinct = distinctSymbols(matches);\n    if (distinct.length === 1) found.push({ file: distinct[0].file, symbol: distinct[0].symbol, label: distinct[0].label, reason: ref.reason });\n    else if (distinct.length > 1) {\n      ambiguous.push(`${ref.card} (${distinct.map((d) => d.cardId ?? `${d.file ?? \"\"}#${d.symbol}`).join(\", \")})`);\n    } else unknown.push(ref.card);\n  }\n  if (unknown.length || ambiguous.length) {\n    const parts = [\n      ...(unknown.length ? [`not among the cards or staged symbols of '${changesetName}': ${unknown.join(\", \")}`] : []),\n      ...(ambiguous.length ? [`names more than one card: ${ambiguous.join(\"; \")}`] : []),\n    ];\n    throw new CLIError(`Can't reject: ${parts.join(\"; \")}. Nothing was recorded`, ErrorCategory.USER, [\n      \"Pass the cardId (or file#symbol) of a card, or the id of an element this extraction staged\",\n    ]);\n  }\n  return found;\n}\n\n/** Drop decisions: all, or those whose key, symbol or file#symbol is listed. Returns how many. */\nfunction clearDecisions(decisions: DecisionsFile, which: true | string[]): number {\n  let n = 0;\n  for (const [key, d] of Object.entries(decisions.notElements)) {\n    if (which === true || which.some((w) => w === key || w === d.symbol || w === `${d.file ?? \"\"}#${d.symbol}`)) {\n      delete decisions.notElements[key];\n      n++;\n    }\n  }\n  return n;\n}\n\nexport function createCodebaseExtractHandler(deps: CodebaseToolDeps = defaultCodebaseToolDeps) {\n  return async function codebaseExtractHandler(args: CodebaseExtractArgs, context?: McpToolContext): Promise<CallToolResult> {\n    return runTool(async () => {\n      const startedAt = Date.now();\n      const deadline = startedAt + (deps.budgetMs ?? DEFAULT_BUDGET_MS);\n      const model = await loadModel(args.rootPath);\n      const { projectRoot, codebaseRoot } = await canonicalRoots(model);\n\n      const argLayers = args.layers?.length ? [...new Set(args.layers)] : undefined;\n      const unknownLayers = (argLayers ?? []).filter((l) => !isValidLayer(l));\n      if (unknownLayers.length) {\n        throw new CLIError(`Unknown layer${unknownLayers.length > 1 ? \"s\" : \"\"}: ${unknownLayers.join(\", \")}`, ErrorCategory.USER, [\n          `Use canonical layer names: ${formatValidOptions(getAllLayerIds())}`,\n        ]);\n      }\n\n      const { analyzer, freshness, index: indexJudgement } = await requireFreshIndex(projectRoot, codebaseRoot, deps, \"codebase_extract\", {\n        uncommittedEdits: true,\n      });\n      const head = freshness.currentGitHead;\n\n      const manager = new StagingAreaManager(model.rootPath, model);\n      const pageSize = args.pageSize ?? DEFAULT_PAGE_SIZE;\n      const effectivePageSize = Math.min(pageSize, MAX_PAGE_SIZE);\n      const baseModified = model.manifest.modified;\n      const paging = (args.page ?? 1) > 1;\n      // A call that only rejects cards or clears decisions records them and runs nothing.\n      const decisionsOnly = !paging && (!!args.reject?.length || args.clearRejected !== undefined);\n\n      // The changeset: the one named; else, for a page or decisions call, the active extraction\n      // changeset (it has a cards file); else the default name for this commit (and range).\n      let name = args.changeset ?? \"\";\n      let changeset: Changeset | null = args.changeset ? await manager.load(args.changeset) : null;\n      if (!args.changeset && (paging || decisionsOnly)) {\n        const activeId = await manager.getActiveId();\n        const active = activeId ? await manager.load(activeId) : null;\n        if (active?.status === \"staged\" && existsSync(cardsPath(projectRoot, active.id!))) {\n          changeset = active;\n          name = active.name;\n        } else {\n          // The extraction changeset isn't the active one (the agent switched back to its plan):\n          // the run at this commit into a staged changeset, when there is only one. With several,\n          // guessing could reject (and unstage) from the wrong one, so the call is refused.\n          const runs = await runsAt(projectRoot, manager, head);\n          if (runs.length === 1) {\n            changeset = runs[0];\n            name = runs[0].name;\n          } else if (runs.length > 1) {\n            throw new CLIError(\n              `Several extraction changesets have runs at this commit (${runs.map((r) => `'${r.name}'`).sort().join(\", \")}), and none is active`,\n              ErrorCategory.USER,\n              [\"Pass changeset with the name of the one you mean\"]\n            );\n          }\n        }\n      }\n      // The last run that staged nothing made no changeset; its cards wait under its name until\n      // that changeset exists (the agent creates it to stage its decisions), which adopts them.\n      // Cards read at another commit are stale: not adopted (their since would be another run's),\n      // and removed under the lock below.\n      const pendingRecord = await readJson<StoredCards>(path.join(extractDir(projectRoot), PENDING_FILE));\n      const pending = pendingRecord?.pending && pendingRecord.gitHead === head ? pendingRecord : null;\n      const stalePending = !!pendingRecord?.pending && pendingRecord.gitHead !== head;\n      const pendingFor = (n: string | undefined) => (pending && n && pending.changesetName === n ? pending : null);\n      let stored = changeset ? await readJson<StoredCards>(cardsPath(projectRoot, changeset.id!)) : null;\n      stored ??= pendingFor(changeset?.name ?? args.changeset);\n      if (\n        !args.changeset &&\n        (paging || decisionsOnly) &&\n        pending &&\n        (!changeset || !stored || stored.createdAt < pending.createdAt)\n      ) {\n        // A page or decisions call after a run that made no changeset (later than the active\n        // extraction changeset's last run): that run's cards, in the changeset of its name once the\n        // agent has created it.\n        const named = await manager.load(pending.changesetName);\n        changeset = named?.status === \"staged\" ? named : null;\n        name = pending.changesetName;\n        stored = pending;\n      }\n\n      // A run or page into an extraction changeset (or the cards waiting for it) keeps its run's\n      // since and layers; a call that names others is refused.\n      let since = args.since;\n      let layers = argLayers;\n      if (stored && (changeset ? changeset.status === \"staged\" : !!stored.pending) && !decisionsOnly) {\n        const conflicts: string[] = [];\n        if (args.since !== undefined && args.since !== (stored.since ?? undefined)) {\n          conflicts.push(`since: ${args.since} (its run had since: ${stored.since ?? \"none\"})`);\n        }\n        if (argLayers && !sameLayers(stored.layers, argLayers)) {\n          conflicts.push(`layers: ${argLayers.join(\", \")} (its run had layers: ${stored.layers?.join(\", \") ?? \"all\"})`);\n        }\n        if (conflicts.length) {\n          throw new CLIError(`'${stored.changesetName}' holds another run's extraction: this call names ${conflicts.join(\" and \")}`, ErrorCategory.USER, [\n            \"Leave since and layers out to use that run's\",\n            \"Or pass another changeset name for a run with these arguments\",\n          ]);\n        }\n        since = stored.since ?? undefined;\n        layers = stored.layers ?? undefined;\n      }\n\n      // The scope: every file, or the files changed since a ref (a run, or a default name to find).\n      let changes: CodeChangesResult | null = null;\n      if (since && (!(paging || decisionsOnly) || (!changeset && !stored))) changes = await (deps.codeChanges ?? codeChangesSince)(codebaseRoot, since);\n\n      if (!changeset && !args.changeset && !stored?.pending) {\n        // A whole-codebase run and a `since` run at the same commit are different changesets. A\n        // range with no commits (only uncommitted edits) is named for the working tree.\n        const defaultName = !changes\n          ? `extract-${head.slice(0, 7)}`\n          : changes.base === head\n            ? `extract-${head.slice(0, 7)}+worktree`\n            : `extract-${changes.base.slice(0, 7)}..${head.slice(0, 7)}`;\n        name = defaultName;\n        changeset = await manager.load(name);\n        // A default name already landed (or discarded) at this commit: take the next free one.\n        for (let n = 2; changeset && changeset.status !== \"staged\"; n++) {\n          name = `${defaultName}-${n}`;\n          changeset = await manager.load(name);\n        }\n        stored = (changeset ? await readJson<StoredCards>(cardsPath(projectRoot, changeset.id!)) : null) ?? pendingFor(name);\n      }\n      if (changeset && changeset.status !== \"staged\") {\n        throw new CLIError(`Changeset '${changeset.name}' is ${changeset.status} and can't take the extraction`, ErrorCategory.USER, [\n          \"Pass another name in changeset\",\n        ]);\n      }\n\n      const backend = paging || decisionsOnly ? null : await deps.getAnalyzer(analyzer);\n      if (!paging && !decisionsOnly) {\n        if (!backend) throw analyzerNotFoundError(analyzer);\n        if (!backend.extract) {\n          throw new CLIError(`The ${analyzer} analyzer can't extract (it has no Tier-0 rules)`, ErrorCategory.USER);\n        }\n      }\n\n      // One call per project at a time, from reading the decisions and the model to staging.\n      await mkdir(extractDir(projectRoot), { recursive: true });\n      const lock = new FileLock(path.join(extractDir(projectRoot), \"run\"));\n      try {\n        await lock.acquire({ timeout: 2000, staleLockThreshold: (deps.budgetMs ?? DEFAULT_BUDGET_MS) + 60_000 });\n      } catch {\n        throw new CLIError(\"Another codebase_extract run is in progress for this project\", ErrorCategory.USER, [\n          \"Wait for it to finish, then call codebase_extract again\",\n        ]);\n      }\n      try {\n        // Decisions, read under the lock: drop inferred ones whose changeset is gone, then what\n        // this call clears, then what it rejects.\n        if (stalePending) {\n          const again = await readJson<StoredCards>(path.join(extractDir(projectRoot), PENDING_FILE));\n          if (again?.pending && again.gitHead !== head) await rm(path.join(extractDir(projectRoot), PENDING_FILE), { force: true });\n        }\n        const decisions = await readDecisions(projectRoot);\n        const stagedIds = new Set((await manager.list()).filter((c) => c.status === \"staged\").map((c) => c.id));\n        let pruned = false;\n        for (const [key, d] of Object.entries(decisions.notElements)) {\n          if (d.how === \"unstaged\" && !(d.changesetId && stagedIds.has(d.changesetId))) {\n            delete decisions.notElements[key];\n            pruned = true;\n          }\n        }\n        const recordedNow: Array<{ symbol: string; file: string | null; how: NotElementDecision[\"how\"] }> = [];\n        let cleared = 0;\n        if (args.clearRejected) cleared = clearDecisions(decisions, args.clearRejected);\n        // What a reject names that is staged in the extraction changeset now: unstaged below, after\n        // recording. Only a changeset this extraction stages into (it has cards, or adopted the\n        // waiting ones) is touched, and in it only extracted elements.\n        const toUnstage = new Map<string, string>();\n        const inBase: string[] = [];\n        const keptElements: Array<{ id: string; alsoNames: string[] }> = [];\n        if (args.reject?.length) {\n          const now = new Date().toISOString();\n          const extractionChangeset = changeset && stored ? changeset : null;\n          const graph = extractionChangeset ? await ChangesetGraph.build(model, extractionChangeset) : null;\n          const rejected = cardsToReject(stored, changesetRejectables(extractionChangeset, graph), changeset?.name ?? stored?.changesetName ?? name, args.reject);\n          const rejectedKeys = new Map<string, string>();\n          for (const card of rejected) {\n            const key = decisionKey(card.file, card.symbol);\n            rejectedKeys.set(key, card.symbol);\n            decisions.notElements[key] = {\n              file: card.file,\n              symbol: card.symbol,\n              ...(card.label ? { label: card.label } : {}),\n              reason: card.reason,\n              how: \"rejected\",\n              changeset: changeset?.name ?? stored?.changesetName ?? name,\n              ...(changeset ? { changesetId: changeset.id! } : {}),\n              at: now,\n            };\n            recordedNow.push({ symbol: card.symbol, file: card.file, how: \"rejected\" });\n          }\n          // Elements that name a rejected symbol. One the changeset adds is unstaged when every\n          // symbol it names is rejected; one that also names other code stays, and is listed. One\n          // the base model has stays (rejecting is about what extraction stages, not what the\n          // model says).\n          const stagedByExtraction = new Map<string, string>();\n          for (const st of stored?.staged ?? []) {\n            const key = decisionKey(st.file, st.symbol);\n            if (rejectedKeys.has(key)) stagedByExtraction.set(st.id, key);\n          }\n          for (const e of graph?.elements.values() ?? []) {\n            if (e.status === \"deleted\") continue;\n            const keys = new Set(\n              (e.sourceReference?.locations ?? []).filter((l) => l.symbol).map((l) => decisionKey(normFile(l.file), l.symbol!))\n            );\n            const hit = stagedByExtraction.get(e.id) ?? [...keys].find((k) => rejectedKeys.has(k));\n            if (!hit) continue;\n            if (!stagedByExtraction.has(e.id) && e.sourceReference?.provenance !== \"extracted\") continue;\n            if (e.status !== \"added\" || e.alreadyInBase) {\n              inBase.push(e.id);\n              continue;\n            }\n            const others = [...keys].filter((k) => !rejectedKeys.has(k));\n            if (others.length) keptElements.push({ id: e.id, alsoNames: others });\n            else toUnstage.set(e.id, rejectedKeys.get(hit)!);\n          }\n        }\n        if (pruned || cleared || recordedNow.length) await writeDecisions(projectRoot, decisions);\n        const notElementKeys = new Set(Object.keys(decisions.notElements));\n\n        // Unstage what was rejected while staged, with the relationships staged for it, so the\n        // decision holds now and not only once the changeset lands.\n        const unstaged: Array<{ id: string; symbol: string; changes: number }> = [];\n        const unstageFailed: Array<{ id: string; error: string }> = [];\n        for (const [id, symbol] of toUnstage) {\n          const result = await changesetUnstageHandler({ elementId: id, changesetId: changeset!.id!, rootPath: args.rootPath });\n          const body = JSON.parse((result.content[0] as { text: string }).text) as { unstaged?: unknown[]; error?: string; message?: string };\n          if (result.isError) unstageFailed.push({ id, error: body.error ?? body.message ?? \"unstage failed\" });\n          else if (body.unstaged?.length) unstaged.push({ id, symbol, changes: body.unstaged.length });\n        }\n        if (unstaged.length && stored && changeset) {\n          // The record of what extraction staged no longer holds what was unstaged. Waiting cards\n          // become this changeset's record here (adopted, as a run would adopt them).\n          const gone = new Set(unstaged.map((u) => u.id));\n          const { pending: wasPending, ...rest } = stored;\n          const updated = (stored.updated ?? []).filter((u) => !gone.has(u.id));\n          stored = {\n            ...rest,\n            changesetId: changeset.id!,\n            changesetName: changeset.name,\n            staged: (stored.staged ?? []).filter((s) => !gone.has(s.id)),\n            ...(updated.length ? { updated } : { updated: undefined }),\n          };\n          await writeFile(cardsPath(projectRoot, changeset.id!), JSON.stringify(stored), \"utf-8\");\n          if (wasPending) await rm(path.join(extractDir(projectRoot), PENDING_FILE), { force: true });\n        }\n        if (unstaged.length) await reloadModel(args.rootPath);\n        const rejectResult = {\n          ...(unstaged.length\n            ? {\n                unstaged: {\n                  items: unstaged,\n                  note: `Rejected while staged: unstaged from '${changeset!.name}', with the relationships staged for them (changes counts both).`,\n                },\n              }\n            : {}),\n          ...(unstageFailed.length ? { unstageFailed } : {}),\n          ...(inBase.length\n            ? { inModel: { ids: [...new Set(inBase)], note: \"Already in the base model: rejecting doesn't remove them. model_delete them if they should go.\" } }\n            : {}),\n          ...(keptElements.length\n            ? {\n                kept: {\n                  items: keptElements,\n                  note: \"Still staged: each also names code that wasn't rejected (alsoNames). Unstage it with changeset_unstage, or drop the rejected location with model_update, if it should change.\",\n                },\n              }\n            : {}),\n        };\n\n        if (decisionsOnly) {\n          const rerunName = changeset?.name ?? stored?.changesetName;\n          const rerun = rerunName ? `changeset: \"${rerunName}\"` : \"the arguments of the last run\";\n          return jsonResult(\n            {\n              changeset: changeset ? { id: changeset.id, name: changeset.name } : null,\n              ...notElementsResult(decisions, 0, recordedNow, cleared),\n              ...rejectResult,\n              message: unstaged.length\n                ? `Recorded, and unstaged ${unstaged.length} element(s) it had staged; nothing was extracted.`\n                : \"Recorded; nothing was extracted or staged.\",\n              next: [`Call codebase_extract with ${rerun} to refresh the cards: it leaves out what is recorded, and says how many.`],\n            },\n            { compact: true }\n          );\n        }\n\n        // Later pages: the last run's cards, marking any the agent has modelled since.\n        if (paging) {\n          if (!stored) {\n            throw new CLIError(\n              changeset ? `No cards recorded for '${changeset.name}'` : `No extraction changeset '${name}' yet`,\n              ErrorCategory.USER,\n              [\"Call codebase_extract without page first\"]\n            );\n          }\n          const runName = changeset?.name ?? stored.changesetName;\n          if (stored.gitHead !== head) {\n            throw new CLIError(`The cards for '${runName}' were read at ${stored.gitHead.slice(0, 7)}; the code is now at ${head.slice(0, 7)}`, ErrorCategory.USER, [\n              \"Call codebase_extract without page to extract again\",\n            ]);\n          }\n          const graph = await ChangesetGraph.build(model, changeset ?? emptyChangeset());\n          const modelledAt = new Map<string, string>();\n          for (const e of graph.elements.values()) {\n            if (e.status === \"deleted\") continue;\n            for (const l of e.sourceReference?.locations ?? []) if (l.symbol) modelledAt.set(`${l.file}#${l.symbol}`, e.id);\n          }\n          const cards = stored.cards\n            .filter((c) => !notElementKeys.has(decisionKey(c.file, c.symbol)))\n            .map((c) => {\n              const modelled = c.file ? modelledAt.get(`${c.file}#${c.symbol}`) : undefined;\n              return modelled ? { ...c, modelled } : c;\n            });\n          const p = page(cards, args.page!, effectivePageSize);\n          return jsonResult(\n            fitCards(p.items, p, (items, fit) => ({\n              changeset: changeset ? { id: changeset.id, name: changeset.name } : null,\n              ...(changeset ? {} : { pending: `No changeset yet: the run that read these cards staged nothing. Call changeset_create with name: \"${runName}\" before staging.` }),\n              ...fitNotes(fit),\n              scope: { since: stored!.since, layers: stored!.layers ?? \"all\" },\n              undecided: undecidedSection(p, items, fit, pageSize),\n              ...notElementsResult(decisions, stored!.cards.length - cards.length, recordedNow, cleared, fit.listLimit),\n              ...rejectResult,\n              ...(stored!.baseModified !== baseModified\n                ? { warning: \"The base model changed since these cards were read; call codebase_extract without page to refresh them.\" }\n                : {}),\n              ...(fit.readOn\n                ? { next: `This page was cut to keep the response small: for the cards after it, ${fit.readOn}.` }\n                : args.page! < p.pages\n                  ? { next: `Call codebase_extract with page: ${args.page! + 1} for the next cards.` }\n                  : {}),\n            })),\n            { compact: true }\n          );\n        }\n        // Uncommitted source edits, deletes and renames the index hasn't seen, from the shared\n        // freshness rule (judgeIndex, which honours deps.sourceEdits).\n        const edited = indexJudgement.editedSince;\n\n        // What the model has: the base, plus the extraction changeset's own changes when it exists.\n        const before = await ChangesetGraph.build(model, changeset ?? emptyChangeset());\n        const referenced = new Set<string>();\n        const liveKeys = new Set<string>();\n        const liveIds = new Set<string>();\n        // The elements this changeset adds, by the symbols they name: a card the agent staged.\n        const addedAt = new Map<string, string>();\n        for (const e of before.elements.values()) {\n          if (e.status === \"deleted\") continue;\n          liveIds.add(e.id);\n          for (const l of e.sourceReference?.locations ?? []) {\n            const file = l.file?.replace(/\\\\/g, \"/\").replace(/^\\.\\//, \"\");\n            if (file) referenced.add(file);\n            if (!l.symbol) continue;\n            const key = decisionKey(file || null, l.symbol);\n            liveKeys.add(key);\n            if (e.status === \"added\" && !e.alreadyInBase && !addedAt.has(key)) addedAt.set(key, e.id);\n          }\n        }\n\n        // Elements this tool staged into the changeset that the agent unstaged from it (the\n        // changeset keeps a tombstone of the unstaged add): not elements, while it stays staged.\n        const storedBefore = stored;\n        const unstagedAdds = new Set(\n          (changeset?.unstaged ?? []).filter((t) => !t.rewritten && t.change.type === \"add\").map((t) => t.change.elementId)\n        );\n        const stillStaged: StagedBySymbol[] = [];\n        for (const st of storedBefore?.staged ?? []) {\n          const key = decisionKey(st.file, st.symbol);\n          if (liveIds.has(st.id) || liveKeys.has(key)) {\n            stillStaged.push(st);\n          } else if (unstagedAdds.has(st.id) && !decisions.notElements[key]) {\n            decisions.notElements[key] = {\n              file: st.file,\n              symbol: st.symbol,\n              label: st.label,\n              reason: `${st.id} was staged by codebase_extract and then unstaged`,\n              how: \"unstaged\",\n              changeset: changeset!.name,\n              changesetId: changeset!.id!,\n              at: new Date().toISOString(),\n            };\n            notElementKeys.add(key);\n            recordedNow.push({ symbol: st.symbol, file: st.file, how: \"unstaged\" });\n          }\n        }\n        // Cards of earlier runs the agent has staged since (model_add with the card's file and\n        // symbol): recorded with the element staged for them, so the record of what extraction\n        // staged covers what came from its cards too (changeset_verify reads it).\n        const recorded = new Set(stillStaged.map((st) => `${st.id} ${decisionKey(st.file, st.symbol)}`));\n        for (const c of [...(storedBefore?.cards ?? []), ...(storedBefore?.earlierCards ?? [])]) {\n          const key = decisionKey(c.file, c.symbol);\n          const id = addedAt.get(key);\n          if (!id || recorded.has(`${id} ${key}`)) continue;\n          recorded.add(`${id} ${key}`);\n          const element = before.getElement(id);\n          stillStaged.push({ id, file: c.file, symbol: c.symbol, label: c.label, ...stagedAs(element?.name, element?.attributes) });\n        }\n        if (recordedNow.some((r) => r.how === \"unstaged\")) await writeDecisions(projectRoot, decisions);\n\n        // With since: only code. DR's own folders are out already; leave out files that are not\n        // source and that no element names (configs, docs, lockfiles).\n        if (changes) {\n          const drDirs = [path.join(projectRoot, \"documentation-robotics\"), path.join(projectRoot, \".dr\")]\n            .map((d) => path.relative(codebaseRoot, d).split(path.sep).join(\"/\"))\n            .filter((d) => d && !d.startsWith(\"..\"));\n          changes = scopeChanges(changes, (f) => !inDirs(f, drDirs) && ((SOURCE_EXT.test(f) && !VENDOR_EXCLUDE.test(f)) || referenced.has(f)));\n        }\n\n        const checkFiles = new Set<string>();\n        for (const e of before.elements.values()) {\n          if (e.status === \"deleted\" || (layers && !layers.includes(e.layer))) continue;\n          for (const l of e.sourceReference?.locations ?? []) {\n            const file = l.file?.replace(/\\\\/g, \"/\").replace(/^\\.\\//, \"\");\n            if (file && l.symbol && (!changes || changes.changed.has(file))) checkFiles.add(file);\n          }\n        }\n\n        let extraction: ExtractionGraph;\n        try {\n          extraction = await backend!.extract!(projectRoot, {\n            codebaseRoot,\n            ...(changes ? { files: changes.changed } : {}),\n            checkFiles: [...checkFiles],\n            deadline,\n          });\n        } catch (error) {\n          if (error instanceof ExtractionTimeoutError) {\n            throw new CLIError(`codebase_extract ran past its ${Math.round((deadline - startedAt) / 1000)} s budget ${error.stage}; nothing was staged`, ErrorCategory.USER, [NARROW]);\n          }\n          throw error;\n        }\n\n        const descriptionsFile = path.join(extractDir(projectRoot), DESCRIPTIONS_FILE);\n        const extractedDescriptions = (await readJson<Record<string, string>>(descriptionsFile)) ?? {};\n        const plan = planElements(extraction, before, {\n          layers,\n          changes,\n          extractedDescriptions,\n          notElements: notElementKeys,\n          fileExists: (file) => existsSync(path.join(codebaseRoot, file)),\n          fileText: (file) => {\n            try {\n              return readFileSync(path.join(codebaseRoot, file), \"utf-8\");\n            } catch {\n              return null;\n            }\n          },\n        });\n\n        const now = new Date().toISOString();\n        const { valid, invalid } = await validateAdds(plan.adds, extraction.project, now, changes?.hunks);\n        const adds = valid.map((v) => v.add);\n        const undecided = sortUndecided(attributeChangedLines([...plan.undecided, ...invalid], changes?.hunks));\n        const kept = new Set(adds);\n        for (const add of plan.adds) {\n          if (!kept.has(add)) {\n            plan.elementOf.delete(add.symbol.qualifiedName);\n            delete plan.descriptions[add.id];\n          }\n        }\n\n        const elements = new Map<string, { layer: string; type: string }>();\n        for (const e of before.elements.values()) if (e.status !== \"deleted\") elements.set(e.id, { layer: e.layer, type: e.type });\n        for (const a of adds) elements.set(a.id, { layer: a.layer, type: a.type });\n        const { relationships, alreadyPresent } = planRelationships(extraction, before, plan.elementOf, elements, hasTriple, layers);\n\n        // Everything staged in one write: adds, updates (an update of an element this changeset\n        // adds rewrites the add in place), relationships.\n        const batch: Array<Omit<StagedChange, \"sequenceNumber\">> = [];\n        const rewrites: Array<{ elementId: string; change: Omit<StagedChange, \"sequenceNumber\"> }> = [];\n        for (const { add, element } of valid) {\n          batch.push({ type: \"add\", elementId: add.id, layerName: add.layer, after: element.toJSON() as unknown as Record<string, unknown> });\n        }\n        const stagedUpdates: PlannedUpdate[] = [];\n        for (const update of plan.updates) {\n          const current = await currentSnapshot(model, before, changeset ?? emptyChangeset(), update.id, update.layer);\n          if (!current) continue;\n          const after = patched(current.snapshot, update, now);\n          if (current.stagedAdd) {\n            rewrites.push({\n              elementId: current.stagedAdd.elementId,\n              change: {\n                type: \"add\",\n                elementId: current.stagedAdd.elementId,\n                layerName: current.stagedAdd.layerName,\n                ...(current.stagedAdd.before !== undefined ? { before: current.stagedAdd.before } : {}),\n                after,\n              },\n            });\n          } else {\n            batch.push({ type: \"update\", elementId: update.id, layerName: update.layer, before: current.snapshot, after });\n          }\n          stagedUpdates.push(update);\n        }\n        for (const r of relationships) batch.push(relationshipChange(r));\n\n        const summary = {\n          adds: adds.length,\n          updates: stagedUpdates.length,\n          relationships: relationships.length,\n          cards: undecided.length,\n          candidateDeletes: plan.candidateDeletes.length,\n        };\n        if (Date.now() > deadline) {\n          throw new CLIError(\n            `codebase_extract ran past its ${Math.round((deadline - startedAt) / 1000)} s budget before staging. It had planned ${summary.adds} adds, ` +\n              `${summary.updates} updates and ${summary.relationships} relationships, with ${summary.cards} cards; nothing was staged`,\n            ErrorCategory.USER,\n            [NARROW]\n          );\n        }\n        if (context?.signal?.aborted) {\n          throw new CLIError(\"codebase_extract was cancelled before staging; nothing was staged\", ErrorCategory.USER);\n        }\n\n        // The changeset active before: the one active now, or (on a later run, when the extraction\n        // changeset is already active) the one the first run replaced, while it is still staged.\n        const activeId = await manager.getActiveId();\n        let previousActive: { id: string; name: string } | null = null;\n        if (activeId && activeId !== changeset?.id) {\n          const prev = await manager.load(activeId);\n          previousActive = { id: activeId, name: prev?.name ?? activeId };\n        } else if (storedBefore?.previousActive) {\n          const prev = await manager.load(storedBefore.previousActive.id);\n          if (prev?.status === \"staged\") previousActive = { id: prev.id!, name: prev.name };\n        }\n        // The record keeps the plan the first run replaced: that is the plan this as-built side\n        // verifies, even when a later run happens while another changeset is active. The next\n        // steps verify against it too; the result's previousActive still says what this run replaced.\n        let recordedPrevious = previousActive;\n        if (storedBefore?.previousActive && storedBefore.previousActive.id !== previousActive?.id) {\n          const first = await manager.load(storedBefore.previousActive.id);\n          if (first?.status === \"staged\") recordedPrevious = { id: first.id!, name: first.name };\n        }\n\n        // A run makes a changeset only to stage into it: a run that stages nothing leaves its cards\n        // and candidate deletes for the agent without creating or activating an empty changeset\n        // (which would then sit in project_status as the next thing to resume).\n        const stages = batch.length > 0 || rewrites.length > 0;\n        const hasWork = stages || undecided.length > 0 || plan.candidateDeletes.length > 0;\n        let created = false;\n        let active = !!changeset && activeId === changeset.id;\n        if (changeset ? hasWork : stages) {\n          if (!changeset) {\n            changeset = await manager.create(\n              name,\n              `As-built extraction of the code at ${head.slice(0, 7)}${since ? `, files changed since ${since}` : \"\"}. Staged by codebase_extract.`\n            );\n            created = true;\n          }\n          try {\n            await manager.stageMany(changeset.id!, batch, rewrites);\n          } catch (error) {\n            // A changeset this run made and couldn't fill is not left behind.\n            if (created) await manager.delete(changeset.id!).catch(() => undefined);\n            throw error;\n          }\n          // Activate last, once staging has succeeded.\n          if (activeId !== changeset.id) await manager.setActive(changeset.id!);\n          active = true;\n          await reloadModel(args.rootPath);\n          if (Object.keys(plan.descriptions).length) {\n            await writeFile(descriptionsFile, JSON.stringify({ ...extractedDescriptions, ...plan.descriptions }), \"utf-8\");\n          }\n        }\n        // Cards earlier runs returned that this one doesn't (the agent modelled them), so reject\n        // can still name them.\n        const nowCards = new Set(undecided.map((c) => c.cardId));\n        const earlierCards = new Map<string, EarlierCard>();\n        for (const c of [...(storedBefore?.earlierCards ?? []), ...(storedBefore?.cards ?? [])]) {\n          // The whole card (candidates, name, proposed), so verify can check type and name against it.\n          if (!nowCards.has(c.cardId)) earlierCards.set(c.cardId, c);\n        }\n        // Updates extraction staged: earlier runs' while their change is still staged, merged with\n        // this run's, one entry per element with the union of its fields and the value extraction\n        // wrote for each (this run's wins), so verify can tell a later hand edit from it.\n        const updatedFields = new Map<string, Map<string, unknown>>();\n        for (const u of storedBefore?.updated ?? []) {\n          const status = before.getElement(u.id)?.status;\n          if (status !== \"updated\" && status !== \"added\") continue;\n          updatedFields.set(u.id, new Map(u.fields.map((f) => [f, u.values && Object.prototype.hasOwnProperty.call(u.values, f) ? u.values[f] : undefined])));\n        }\n        for (const u of stagedUpdates) {\n          const fields = updatedFields.get(u.id) ?? updatedFields.set(u.id, new Map()).get(u.id)!;\n          for (const [f, value] of Object.entries(u.fields)) fields.set(f, structuredClone(value));\n        }\n        const updatedRecord = [...updatedFields].map(([id, fields]) => {\n          const names = [...fields.keys()].sort();\n          const values = Object.fromEntries(names.filter((f) => fields.get(f) !== undefined).map((f) => [f, fields.get(f)]));\n          return { id, fields: names, ...(Object.keys(values).length ? { values } : {}) };\n        });\n        const candidateDeleteIds = [...new Set([...(storedBefore?.candidateDeletes ?? []), ...plan.candidateDeletes.map((d) => d.id)])];\n        const accumulated = {\n          ...(updatedRecord.length ? { updated: updatedRecord } : {}),\n          ...(candidateDeleteIds.length ? { candidateDeletes: candidateDeleteIds } : {}),\n        };\n        const pendingPath = path.join(extractDir(projectRoot), PENDING_FILE);\n        if (changeset) {\n          const staged = [...stillStaged];\n          for (const a of adds) {\n            staged.push({\n              id: a.id,\n              file: a.symbol.card.file_path,\n              symbol: sourceSymbolOf(a.symbol, extraction.project),\n              label: a.symbol.card.label,\n              ...stagedAs(a.name, a.attributes),\n            });\n          }\n          const record: StoredCards = {\n            changesetId: changeset.id!,\n            changesetName: changeset.name,\n            gitHead: head,\n            since: since ?? null,\n            layers: layers ?? null,\n            baseModified,\n            previousActive: recordedPrevious,\n            createdAt: now,\n            cards: undecided,\n            staged,\n            ...(earlierCards.size ? { earlierCards: [...earlierCards.values()] } : {}),\n            ...accumulated,\n          };\n          await writeFile(cardsPath(projectRoot, changeset.id!), JSON.stringify(record), \"utf-8\");\n          // Waiting cards this changeset now holds.\n          if (pending?.changesetName === changeset.name) await rm(pendingPath, { force: true });\n        } else if (undecided.length || plan.candidateDeletes.length) {\n          const record: StoredCards = {\n            changesetId: \"\",\n            changesetName: name,\n            gitHead: head,\n            since: since ?? null,\n            layers: layers ?? null,\n            baseModified,\n            previousActive,\n            createdAt: now,\n            cards: undecided,\n            staged: [],\n            ...(earlierCards.size ? { earlierCards: [...earlierCards.values()] } : {}),\n            ...accumulated,\n            pending: true,\n          };\n          await writeFile(pendingPath, JSON.stringify(record), \"utf-8\");\n        } else if (pending?.changesetName === name) {\n          await rm(pendingPath, { force: true });\n        }\n        await pruneCardFiles(projectRoot, manager);\n\n        const cards = page(undecided, 1, effectivePageSize);\n        const changedCards = undecided.filter((c) => c.changedInRange).length;\n        const changesetRef = changeset ? { id: changeset.id!, name: changeset.name } : null;\n        const verifyMode = !!since && !!recordedPrevious;\n        const message = !hasWork\n          ? verifyMode && !changeset\n            ? `Nothing to stage: nothing in the range is observable to extraction or differs from the model. No as-built changeset was created; ${previousActive ? `'${previousActive.name}' is still active.` : `the plan is '${recordedPrevious!.name}'.`}`\n            : changeset\n              ? `Nothing more to stage: '${changeset.name}' already says what this code says.`\n              : \"Nothing to stage: the model already says what this code says. No changeset was created or activated.\"\n          : !changeset\n            ? `Nothing to stage, so no changeset was created or activated. ${undecided.length} card(s)` +\n              `${changedCards ? ` (${changedCards} changed in the range)` : \"\"} and ${plan.candidateDeletes.length} candidate delete(s) are left for you to decide; ` +\n              `to stage any, first call changeset_create with name: \"${name}\".`\n            : undefined;\n        return jsonResult(\n          fitCards(cards.items, cards, (items, fit) => ({\n            changeset: changesetRef ? { ...changesetRef, created, active } : null,\n            previousActive,\n            ...(message ? { message } : {}),\n            ...fitNotes(fit),\n            ...(edited.length\n              ? {\n                  warning:\n                    `${edited.length} source file(s) have uncommitted edits made after the index was taken, which this run may not have seen ` +\n                    `(${edited.slice(0, 5).join(\", \")}${edited.length > 5 ? \", ...\" : \"\"}). Re-index with codebase_index, then call codebase_extract again.`,\n                }\n              : {}),\n            ...(changes?.hunksError\n              ? {\n                  hunksWarning: `The range's changed lines couldn't be read (${changes.hunksError}), so no card says changedInRange; the cards are those of every changed file.`,\n                }\n              : {}),\n            analyzer,\n            // The shared judgement: `fresh-with-uncommitted-edits` when the warning above is given.\n            index: describeIndex(freshness, indexJudgement),\n            scope: {\n              since: since ?? null,\n              ...(changes ? { base: changes.base, changedFiles: changes.changed.size, deletedFiles: changes.deleted.size } : { files: \"all\" }),\n              layers: layers ?? \"all\",\n            },\n            cards: { ...extraction.summary, needsAttributes: invalid.length },\n            staged: {\n              adds: adds.length,\n              updates: stagedUpdates.length,\n              relationships: relationships.length,\n              byLayer: byLayer(adds, stagedUpdates, relationships),\n              ...(stagedUpdates.length ? { updated: capped(stagedUpdates.map((u) => ({ id: u.id, fields: Object.keys(u.fields) })), fit.listLimit) } : {}),\n            },\n            unchanged: {\n              elements: plan.unchanged,\n              modelled: plan.modelled,\n              relationships: alreadyPresent,\n              rejected: plan.rejected,\n              ...(plan.outsideLayers ? { outsideLayers: plan.outsideLayers } : {}),\n            },\n            candidateDeletes: {\n              ...capped(plan.candidateDeletes, fit.listLimit),\n              note: \"Not staged: deleting is left to you. Each has its evidence.\",\n            },\n            ...(plan.retyped.length ? { retyped: capped(plan.retyped, fit.listLimit) } : {}),\n            ...notElementsResult(decisions, plan.skipped, recordedNow, cleared, fit.listLimit),\n            undecided: undecidedSection(cards, items, fit, pageSize, changes ? { changedInRange: changedCards } : {}),\n            tier1: \"not wired: cards Tier 0 can't decide come to you (docs/EXTRACTION_STRATEGY.md, B6)\",\n            durationMs: Date.now() - startedAt,\n            next: !hasWork\n              ? verifyMode\n                ? changesetRef\n                  ? nextSteps(changesetRef, recordedPrevious, 0, plan, 0, since)\n                  : verifyNothingSteps(recordedPrevious!, since!)\n                : []\n              : changesetRef\n                ? nextSteps(changesetRef, recordedPrevious, cards.pages, plan, changedCards, since, fit.readOn)\n                : pendingSteps(name, recordedPrevious, cards.pages, plan, changedCards, since, fit.readOn),\n          })),\n          { compact: true }\n        );\n      } finally {\n        await lock.release().catch(() => undefined);\n      }\n    });\n  };\n}\n\nexport const codebaseExtractHandler = createCodebaseExtractHandler();\n\nexport const codebaseExtractTool: McpToolDefinition<typeof inputSchema> = {\n  name: \"codebase_extract\",\n  description:\n    \"Model the indexed code as an as-built changeset: Tier-0 rules decide what they can and those elements and \" +\n    \"their relationships are staged; the rest come back as undecided cards (paged) for you to stage with model_add. \" +\n    \"Stages only what differs from the model (matched by source file and symbol): new symbols are adds, changed ones \" +\n    \"updates; elements whose code is gone are listed as candidateDeletes, not staged. since (a git ref) limits it to \" +\n    \"files changed since then, for verifying a branch; cards whose lines the range changed say changedInRange and come first. \" +\n    \"Code that is not an element goes in reject (with a reason): a card, or a symbol or element it staged, which is then \" +\n    \"unstaged; kept until clearRejected, later runs leave them out. An element \" +\n    \"it staged that you unstage from a changeset is also left out, but only while that changeset is staged: discarding or \" +\n    \"landing it forgets that. A run or page into an extraction changeset keeps that run's since and layers. \" +\n    \"The changeset (default extract-<sha>) is created and made active only when the run stages something; a run that only \" +\n    \"leaves cards or candidate deletes creates nothing and says which changeset to create first. previousActive is the one \" +\n    \"active before the first run. Needs a fresh index (codebase_index). Never writes the base model or commits.\",\n  inputSchema,\n  handler: codebaseExtractHandler,\n};\n"],
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+  "names": ["result", "byLayer", "now", "cards"]
+}

package/dist/mcp/tools/codebase-index.js

@@ -0,0 +1,125 @@
+import { z } from "zod";
+import { readIndexJob, startIndexJob } from "../../analyzers/index-job.js";
+import { readSession, writeSession } from "../../analyzers/session-state.js";
+import { CLIError, ErrorCategory } from "../../utils/errors.js";
+import { jsonResult, loadModel, rootPathSchema, runTool } from "./shared.js";
+import { analyzerNotFoundError, assessIndex, canonicalRoots, defaultCodebaseToolDeps, describeIndex, installSuggestions, notInstalledError, takeWorktreeSnapshot, WAIT_FOR_INDEX, writeWorktreeSnapshot } from "./codebase-shared.js";
+const MAX_WAIT_SECONDS = 50, inputSchema = {
+  status: z.boolean().optional().describe("Only report the current or last run and the index's freshness; start nothing."),
+  wait: z.number().min(0).optional().describe(`Seconds to block until the run finishes (at most ${MAX_WAIT_SECONDS}; larger values are capped). Returns early when the run ends. Pass 30 when starting and when polling.`),
+  force: z.boolean().optional().describe("Re-index even when the index is fresh. Also stops a run in flight and starts over (for a stuck run)."),
+  rootPath: rootPathSchema
+}, POLL = `Indexing is still running. ${WAIT_FOR_INDEX} or failed; do other work between calls if you have any.`;
+function nextStep(job, freshness, judgement) {
+  if (job?.state === "running")
+    return POLL;
+  const state = judgement?.state ?? "stale";
+  return job?.state === "failed" && state !== "fresh" ? "The last run failed: see job.error and the log at job.logPath. Fix the cause, then call codebase_index again." : freshness.indexed ? state === "fresh" ? "The index is fresh. codebase_extract models the code; codebase_verify checks the API layer's operations against the code's routes." : state === "fresh-with-uncommitted-edits" ? "Source files were edited after the index was taken (index.uncommittedEdits). Call codebase_index with wait: 30 to re-index them." : "The code has changed since the last index. Call codebase_index with wait: 30 to re-index." : "The code is not indexed. Call codebase_index with wait: 30 to index it.";
+}
+const sleep = (ms, signal) => new Promise((resolve) => {
+  const timer = setTimeout(done, ms);
+  function done() {
+    clearTimeout(timer), signal?.removeEventListener("abort", done), resolve();
+  }
+  signal?.addEventListener("abort", done, { once: !0 });
+}), REPORT_RESERVE_MS = 2e3;
+async function waitForJob(projectRoot, job, deadline, deps, signal) {
+  const interval = deps.pollIntervalMs ?? 1e3;
+  let current = job;
+  for (; current?.state === "running" && Date.now() < deadline && !signal?.aborted; )
+    await sleep(Math.max(1, Math.min(interval, deadline - Date.now())), signal), current = await readIndexJob(projectRoot, { isAlive: deps.isAlive });
+  return current;
+}
+function createCodebaseIndexHandler(deps = defaultCodebaseToolDeps) {
+  return async function(args, context) {
+    const deadline = Date.now() + Math.min((args.wait ?? 0) * 1e3, MAX_WAIT_SECONDS * 1e3 - REPORT_RESERVE_MS);
+    return runTool(async () => {
+      const model = await loadModel(args.rootPath), { projectRoot, codebaseRoot } = await canonicalRoots(model), job = await readIndexJob(projectRoot, { isAlive: deps.isAlive }), session = await readSession(projectRoot), report = async (analyzer2, started2, current2, extra = {}) => {
+        const waited = args.wait && args.wait > 0 && current2?.state === "running", startedWaiting = Date.now(), settled = waited ? await waitForJob(projectRoot, current2, deadline, deps, context?.signal) : current2, { freshness, judgement } = analyzer2 ? await assessIndex(projectRoot, analyzer2, codebaseRoot, deps) : { freshness: { indexed: !1, fresh: !1 }, judgement: null };
+        return jsonResult({
+          projectRoot,
+          analyzer: analyzer2,
+          started: started2,
+          job: settled,
+          ...waited ? { waitedSeconds: Math.round((Date.now() - startedWaiting) / 1e3) } : {},
+          index: describeIndex(freshness, judgement),
+          next: nextStep(settled, freshness, judgement),
+          ...extra
+        });
+      };
+      if (args.status)
+        return report(session?.active_analyzer || job?.analyzer || null, !1, job);
+      if (job?.state === "running" && !args.force)
+        return report(job.analyzer, !1, job);
+      let analyzer = session?.active_analyzer, discovered = !1;
+      if (!analyzer) {
+        const discovery = await deps.discover();
+        if (!discovery.selected) {
+          const name = discovery.found[0]?.name ?? "cbm";
+          throw new CLIError("No code analyzer is installed", ErrorCategory.USER, await installSuggestions(name));
+        }
+        analyzer = discovery.selected, discovered = !0, await writeSession({ active_analyzer: analyzer, selected_at: (/* @__PURE__ */ new Date()).toISOString() }, projectRoot);
+      }
+      const backend = await deps.getAnalyzer(analyzer);
+      if (!backend)
+        throw analyzerNotFoundError(analyzer);
+      if (!discovered && !(await backend.detect(projectRoot)).installed)
+        throw await notInstalledError(analyzer);
+      let editedSinceIndex = !1;
+      if (!args.force) {
+        const { judgement } = await assessIndex(projectRoot, analyzer, codebaseRoot, deps);
+        if (judgement?.state === "fresh")
+          return report(analyzer, !1, job, {
+            ...discovered ? { discovered: !0 } : {},
+            message: "The index is fresh; nothing to do. Pass force: true to re-index anyway."
+          });
+        editedSinceIndex = judgement?.state === "fresh-with-uncommitted-edits";
+      }
+      const ignoreFile = analyzer === "cbm" ? await cbmIgnoreFile(codebaseRoot, projectRoot) : void 0, snapshot = await takeWorktreeSnapshot(codebaseRoot), { started, job: current, replaced } = await startIndexJob({
+        projectRoot,
+        codebaseRoot,
+        analyzer,
+        // The child skips an index taken at the current HEAD unless forced; uncommitted edits need the run.
+        force: args.force || editedSinceIndex,
+        replaceRunning: args.force,
+        spawn: deps.spawn,
+        kill: deps.kill,
+        drCommand: deps.drCommand,
+        isAlive: deps.isAlive
+      });
+      return started && snapshot && await writeWorktreeSnapshot(projectRoot, analyzer, { ...snapshot, jobId: current.jobId }).catch(() => {
+      }), report(analyzer, started, current, {
+        ...discovered ? { discovered: !0 } : {},
+        ...replaced ? { replaced } : {},
+        // Said only with a run that started (and will read it), not beside a run that did not.
+        ...ignoreFile && started ? { ignoreFile } : {}
+      });
+    });
+  };
+}
+async function cbmIgnoreFile(codebaseRoot, projectRoot) {
+  try {
+    const { ensureCbmIgnore } = await import("../../analyzers/cbm-analyzer.js"), result = await ensureCbmIgnore(codebaseRoot, projectRoot);
+    return result.added.length === 0 ? void 0 : {
+      path: result.path,
+      created: result.created,
+      added: result.added,
+      note: "codebase-memory-mcp indexes every file it isn't told to skip; this keeps DR's model, changesets and analyzer state out of the index. Commit the file with the code."
+    };
+  } catch (error) {
+    return { error: `Could not update .cbmignore, so DR's own files may be indexed: ${error instanceof Error ? error.message : String(error)}` };
+  }
+}
+const codebaseIndexHandler = createCodebaseIndexHandler(), codebaseIndexTool = {
+  name: "codebase_index",
+  description: `Index the project's code with the code analyzer (codebase-memory-mcp) in the background. Returns the job ({state: running|done|failed, startedAt, finishedAt, error, progress, logPath}) and the index's freshness (index.state: fresh, fresh-with-uncommitted-edits or stale). With wait (seconds, at most ${MAX_WAIT_SECONDS}) it blocks until the run ends or the wait does; without it, it returns at once. Start with wait: 30, then call it with status: true, wait: 30 until job.state is done or failed. A call while a run is in flight returns that run; force: true stops it and starts over. Skips a fresh index unless force: true. Selects an installed analyzer if none is. Writes .dr/analyzers/, and for codebase-memory-mcp a .cbmignore at the codebase root that keeps documentation-robotics/ and .dr/ out of the index (ignoreFile says when it changed it); never the model.`,
+  inputSchema,
+  handler: codebaseIndexHandler
+};
+export {
+  MAX_WAIT_SECONDS,
+  codebaseIndexHandler,
+  codebaseIndexTool,
+  createCodebaseIndexHandler
+};
+//# sourceMappingURL=codebase-index.js.map

package/dist/mcp/tools/codebase-index.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../../src/mcp/tools/codebase-index.ts"],
+  "sourcesContent": ["/**\n * codebase_index \u2014 index the project's code with the analyzer (codebase-memory-mcp), in the\n * background.\n *\n * It starts `dr analyzer index` in a detached process. Without `wait` it returns at once; with\n * `wait` (seconds, capped at MAX_WAIT_SECONDS) it blocks until the run ends or the wait does, then\n * returns the job. The agent repeats `status: true, wait: 30` until the job is done or failed.\n * Indexing a large codebase outlasts an MCP call, and a client that moves a long call to the\n * background (Claude Code after 2 minutes) loses its result under `claude -p`, so a single call\n * never waits longer than about 50 seconds. The job record is `.dr/analyzers/index-job.json`\n * (analyzers/index-job.ts). Writes no model files.\n */\n\nimport { z } from \"zod\";\nimport type { CallToolResult } from \"@modelcontextprotocol/sdk/types.js\";\nimport { readIndexJob, startIndexJob, type IndexJob } from \"../../analyzers/index-job.js\";\nimport { readSession, writeSession } from \"../../analyzers/session-state.js\";\nimport type { IndexFreshness } from \"../../analyzers/active-analyzer.js\";\nimport { CLIError, ErrorCategory } from \"../../utils/errors.js\";\nimport { jsonResult, loadModel, rootPathSchema, runTool, type McpToolContext, type McpToolDefinition } from \"./shared.js\";\nimport {\n  analyzerNotFoundError,\n  assessIndex,\n  canonicalRoots,\n  defaultCodebaseToolDeps,\n  describeIndex,\n  installSuggestions,\n  notInstalledError,\n  takeWorktreeSnapshot,\n  WAIT_FOR_INDEX,\n  writeWorktreeSnapshot,\n  type CodebaseToolDeps,\n  type IndexJudgement,\n} from \"./codebase-shared.js\";\n\n/** The longest one call blocks: under the point where a client moves a call to the background. */\nexport const MAX_WAIT_SECONDS = 50;\n\nconst inputSchema = {\n  status: z\n    .boolean()\n    .optional()\n    .describe(\"Only report the current or last run and the index's freshness; start nothing.\"),\n  wait: z\n    .number()\n    .min(0)\n    .optional()\n    .describe(\n      `Seconds to block until the run finishes (at most ${MAX_WAIT_SECONDS}; larger values are capped). Returns early when the run ends. Pass 30 when starting and when polling.`\n    ),\n  force: z\n    .boolean()\n    .optional()\n    .describe(\"Re-index even when the index is fresh. Also stops a run in flight and starts over (for a stuck run).\"),\n  rootPath: rootPathSchema,\n};\n\nexport type CodebaseIndexArgs = z.infer<z.ZodObject<typeof inputSchema>>;\n\nconst POLL = `Indexing is still running. ${WAIT_FOR_INDEX} or failed; do other work between calls if you have any.`;\n\n/** What the agent should do next, given the job and the index. */\nfunction nextStep(job: IndexJob | null, freshness: IndexFreshness, judgement: IndexJudgement | null): string {\n  if (job?.state === \"running\") return POLL;\n  const state = judgement?.state ?? \"stale\";\n  if (job?.state === \"failed\" && state !== \"fresh\") {\n    return \"The last run failed: see job.error and the log at job.logPath. Fix the cause, then call codebase_index again.\";\n  }\n  if (!freshness.indexed) return \"The code is not indexed. Call codebase_index with wait: 30 to index it.\";\n  if (state === \"fresh\") {\n    return \"The index is fresh. codebase_extract models the code; codebase_verify checks the API layer's operations against the code's routes.\";\n  }\n  if (state === \"fresh-with-uncommitted-edits\") {\n    return \"Source files were edited after the index was taken (index.uncommittedEdits). Call codebase_index with wait: 30 to re-index them.\";\n  }\n  return \"The code has changed since the last index. Call codebase_index with wait: 30 to re-index.\";\n}\n\n/** Sleeps `ms`, or less when `signal` aborts. */\nconst sleep = (ms: number, signal?: AbortSignal) =>\n  new Promise<void>((resolve) => {\n    const timer = setTimeout(done, ms);\n    function done() {\n      clearTimeout(timer);\n      signal?.removeEventListener(\"abort\", done);\n      resolve();\n    }\n    signal?.addEventListener(\"abort\", done, { once: true });\n  });\n\n/** Blocks until the run is no longer running or `seconds` pass, and returns the job as it is then. */\n/** Time kept back from the wait for the last read of the index, so the whole call fits the cap. */\nconst REPORT_RESERVE_MS = 2000;\n\n/**\n * Blocks until the run is no longer running, `deadline` passes, or the request is cancelled, and\n * returns the job as it is then.\n */\nasync function waitForJob(\n  projectRoot: string,\n  job: IndexJob | null,\n  deadline: number,\n  deps: CodebaseToolDeps,\n  signal?: AbortSignal\n): Promise<IndexJob | null> {\n  const interval = deps.pollIntervalMs ?? 1000;\n  let current = job;\n  while (current?.state === \"running\" && Date.now() < deadline && !signal?.aborted) {\n    await sleep(Math.max(1, Math.min(interval, deadline - Date.now())), signal);\n    current = await readIndexJob(projectRoot, { isAlive: deps.isAlive });\n  }\n  return current;\n}\n\nexport function createCodebaseIndexHandler(deps: CodebaseToolDeps = defaultCodebaseToolDeps) {\n  return async function codebaseIndexHandler(args: CodebaseIndexArgs, context?: McpToolContext): Promise<CallToolResult> {\n    // The wait counts from the call's start: loading the model and running git use it up too.\n    const deadline = Date.now() + Math.min((args.wait ?? 0) * 1000, MAX_WAIT_SECONDS * 1000 - REPORT_RESERVE_MS);\n    return runTool(async () => {\n      // The project comes from rootPath or the client's roots (loadModel waits for them).\n      const model = await loadModel(args.rootPath);\n      // One spelling of each root for this call and the child it starts (see canonicalRoots).\n      const { projectRoot, codebaseRoot } = await canonicalRoots(model);\n      const job = await readIndexJob(projectRoot, { isAlive: deps.isAlive });\n      const session = await readSession(projectRoot);\n\n      const report = async (analyzer: string | null, started: boolean, current: IndexJob | null, extra = {}) => {\n        const waited = args.wait && args.wait > 0 && current?.state === \"running\";\n        const startedWaiting = Date.now();\n        const settled = waited ? await waitForJob(projectRoot, current, deadline, deps, context?.signal) : current;\n        const { freshness, judgement } = analyzer\n          ? await assessIndex(projectRoot, analyzer, codebaseRoot, deps)\n          : { freshness: { indexed: false, fresh: false } as const, judgement: null };\n        return jsonResult({\n          projectRoot,\n          analyzer,\n          started,\n          job: settled,\n          ...(waited ? { waitedSeconds: Math.round((Date.now() - startedWaiting) / 1000) } : {}),\n          index: describeIndex(freshness, judgement),\n          next: nextStep(settled, freshness, judgement),\n          ...extra,\n        });\n      };\n\n      if (args.status) {\n        return report(session?.active_analyzer || job?.analyzer || null, false, job);\n      }\n\n      // One run at a time: a call while one is in flight reports that run. force replaces it.\n      if (job?.state === \"running\" && !args.force) {\n        return report(job.analyzer, false, job);\n      }\n\n      // Pick the analyzer, discovering one when none is selected yet.\n      let analyzer = session?.active_analyzer;\n      let discovered = false;\n      if (!analyzer) {\n        const discovery = await deps.discover();\n        if (!discovery.selected) {\n          const name = discovery.found[0]?.name ?? \"cbm\";\n          throw new CLIError(\"No code analyzer is installed\", ErrorCategory.USER, await installSuggestions(name));\n        }\n        analyzer = discovery.selected;\n        discovered = true;\n        await writeSession({ active_analyzer: analyzer, selected_at: new Date().toISOString() }, projectRoot);\n      }\n\n      const backend = await deps.getAnalyzer(analyzer);\n      if (!backend) throw analyzerNotFoundError(analyzer);\n      // Discovery has just checked it; otherwise check before starting a run that would fail.\n      if (!discovered) {\n        const detection = await backend.detect(projectRoot);\n        if (!detection.installed) throw await notInstalledError(analyzer);\n      }\n\n      let editedSinceIndex = false;\n      if (!args.force) {\n        const { judgement } = await assessIndex(projectRoot, analyzer, codebaseRoot, deps);\n        if (judgement?.state === \"fresh\") {\n          return report(analyzer, false, job, {\n            ...(discovered ? { discovered: true } : {}),\n            message: \"The index is fresh; nothing to do. Pass force: true to re-index anyway.\",\n          });\n        }\n        editedSinceIndex = judgement?.state === \"fresh-with-uncommitted-edits\";\n      }\n\n      // codebase-memory-mcp indexes every file it isn't told to skip, DR's changesets and analyzer\n      // state included; the run writes .cbmignore too, but doing it here lets the result say so.\n      const ignoreFile = analyzer === \"cbm\" ? await cbmIgnoreFile(codebaseRoot, projectRoot) : undefined;\n\n      // The uncommitted source files as the run starts, so a later check sees any change to them.\n      const snapshot = await takeWorktreeSnapshot(codebaseRoot);\n      const { started, job: current, replaced } = await startIndexJob({\n        projectRoot,\n        codebaseRoot,\n        analyzer,\n        // The child skips an index taken at the current HEAD unless forced; uncommitted edits need the run.\n        force: args.force || editedSinceIndex,\n        replaceRunning: args.force,\n        spawn: deps.spawn,\n        kill: deps.kill,\n        drCommand: deps.drCommand,\n        isAlive: deps.isAlive,\n      });\n      if (started && snapshot) {\n        await writeWorktreeSnapshot(projectRoot, analyzer, { ...snapshot, jobId: current.jobId }).catch(() => undefined);\n      }\n      return report(analyzer, started, current, {\n        ...(discovered ? { discovered: true } : {}),\n        ...(replaced ? { replaced } : {}),\n        // Said only with a run that started (and will read it), not beside a run that did not.\n        ...(ignoreFile && started ? { ignoreFile } : {}),\n      });\n    });\n  };\n}\n\n/**\n * Adds DR's own folders to the codebase's .cbmignore (cbm-analyzer.ts ensureCbmIgnore), and says\n * what it did when it changed the file, so the agent can tell the developer about a new file to\n * commit. Undefined when nothing changed; a failure is reported, not thrown: the run still works.\n */\nasync function cbmIgnoreFile(codebaseRoot: string, projectRoot: string): Promise<Record<string, unknown> | undefined> {\n  try {\n    const { ensureCbmIgnore } = await import(\"../../analyzers/cbm-analyzer.js\");\n    const result = await ensureCbmIgnore(codebaseRoot, projectRoot);\n    if (result.added.length === 0) return undefined;\n    return {\n      path: result.path,\n      created: result.created,\n      added: result.added,\n      note:\n        \"codebase-memory-mcp indexes every file it isn't told to skip; this keeps DR's model, changesets and analyzer state out of the index. Commit the file with the code.\",\n    };\n  } catch (error) {\n    return { error: `Could not update .cbmignore, so DR's own files may be indexed: ${error instanceof Error ? error.message : String(error)}` };\n  }\n}\n\nexport const codebaseIndexHandler = createCodebaseIndexHandler();\n\nexport const codebaseIndexTool: McpToolDefinition<typeof inputSchema> = {\n  name: \"codebase_index\",\n  description:\n    \"Index the project's code with the code analyzer (codebase-memory-mcp) in the background. Returns the job \" +\n    \"({state: running|done|failed, startedAt, finishedAt, error, progress, logPath}) and the index's freshness \" +\n    \"(index.state: fresh, fresh-with-uncommitted-edits or stale). With wait (seconds, at most \" +\n    `${MAX_WAIT_SECONDS}) it blocks until the run ends or the wait does; without it, it returns at once. Start with ` +\n    \"wait: 30, then call it with status: true, wait: 30 until job.state is done or failed. A call while a run \" +\n    \"is in flight returns that run; force: true stops it and starts over. Skips a fresh index unless force: true. \" +\n    \"Selects an installed analyzer if none is. Writes .dr/analyzers/, and for codebase-memory-mcp a .cbmignore at \" +\n    \"the codebase root that keeps documentation-robotics/ and .dr/ out of the index (ignoreFile says when it changed \" +\n    \"it); never the model.\",\n  inputSchema,\n  handler: codebaseIndexHandler,\n};\n"],
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+}