@hawkeyexl/manni 4.5.0 → 4.6.0

package/dist/{cli-HUIMNJT6.js.map → cli-EPVZHAZS.js.map}

@@ -1 +1 @@
-{"version":3,"sources":["../src/graph/cli.ts","../src/graph/reporters/index.ts","../src/graph/commands/init.ts"],"sourcesContent":["/**\n * The graph program. Named `graph` because that is where it is mounted\n * (`manni graph …`); `src/cli.ts` adds it to the umbrella and runs it.\n *\n * Grammar per proposals 0034 and 0051 §2: the domain owns verbs and has no\n * default subcommand, `-f` means the output format everywhere and is checked\n * against the verb's list, and a list reaches a flag by exactly one\n * separator. The plumbing is the family's: `fail()` from `src/shared/run.ts`,\n * `warn()` from `src/shared/warn.ts`, and `--no-color` from\n * `src/shared/color.ts`.\n */\nimport { Command } from \"commander\";\nimport pkg from \"../../package.json\" with { type: \"json\" };\nimport {\n  collect,\n  configOption,\n  readStdin,\n  splitList,\n} from \"../shared/cli-options.js\";\nimport { shouldColor } from \"../shared/color.js\";\nimport { fail } from \"../shared/run.js\";\nimport { warn } from \"../shared/warn.js\";\nimport { GraphError } from \"./types.js\";\nimport { LOCAL_FLAG_HELP } from \"../shared/providers.js\";\nimport { ALL_FILL_FIELDS, type FillField } from \"./core/config.js\";\nimport {\n  assertInputFormat,\n  DEFAULT_EXTENSIONS,\n  STDIN,\n} from \"./core/discover.js\";\nimport {\n  CHECK_FORMATS,\n  CHECK_FORMAT_LIST,\n  GRAPH_FORMATS,\n  GRAPH_FORMAT_LIST,\n  type CheckFormat,\n  type GraphFormat,\n} from \"./reporters/index.js\";\nimport { runBuild } from \"./commands/build.js\";\nimport { renderCheck, runCheck } from \"./commands/check.js\";\nimport {\n  EXPORT_TARGETS,\n  runExport,\n  type ExportFormat,\n} from \"./commands/export.js\";\nimport { renderQuery, runQuery } from \"./commands/query.js\";\nimport { renderFill, runFill } from \"./commands/fill.js\";\nimport { runInit } from \"./commands/init.js\";\nimport { renderEmbed, runEmbed } from \"./commands/embed.js\";\nimport {\n  renderSearch,\n  runSearch,\n  SEARCH_MODES,\n  type SearchMode,\n} from \"./commands/search.js\";\nimport { renderStats, runStats } from \"./commands/stats.js\";\nimport { renderTraverse, runTraverse } from \"./commands/traverse.js\";\n\n/**\n * Whether `command`'s output gets colour: this domain's `--no-color` and\n * `NO_COLOR` turn it off, and otherwise only a TTY turns it on\n * (`shouldColor`). `isTTY` is passed uncoerced: Node leaves it undefined off\n * a terminal, never false, and `shouldColor` reads a missing one as \"not a\n * terminal\".\n *\n * Exported because this is where the decision is testable — a spawned bin is\n * never a TTY. graph's reporters print no colour yet; when one does, it takes\n * the boolean from here rather than consulting the environment itself.\n */\nexport function colorFor(\n  command: Command,\n  isTTY: boolean | undefined,\n  env?: NodeJS.ProcessEnv,\n): boolean {\n  // commander maps --no-color to opts.color === false, on the command that\n  // declares it.\n  const noColor = colorOwner(command).opts().color === false;\n  return shouldColor({ noColor, isTTY, env });\n}\n\n/**\n * The nearest command, this one or an ancestor, that declares `--no-color`:\n * the `graph` program, wherever it is mounted. Not the root: under the umbrella\n * that is `manni`, which has no `--no-color` of its own.\n */\nfunction colorOwner(command: Command): Command {\n  for (let c: Command | null = command; c !== null; c = c.parent) {\n    if (c.options.some((o) => o.long === \"--no-color\")) return c;\n  }\n  return command;\n}\n\nexport function buildProgram(): Command {\nconst program = new Command();\n\nprogram\n  .name(\"graph\")\n  .description(\n    \"Deterministic knowledge graphs derived from documentation frontmatter and formatting.\",\n  )\n  .version(pkg.version)\n  .option(\"--no-color\", \"disable colored output\")\n  // A pointer, not the whole help screen: the message that precedes it\n  // already names the offending flag.\n  .showHelpAfterError(\"(add --help for usage)\")\n  // MUST come before the `.command()` calls below. `copyInheritedSettings`\n  // copies `_exitCallback` by value at subcommand-creation time, so an\n  // `exitOverride()` installed afterwards leaves every subcommand still\n  // calling `process.exit(1)` — which reports a usage error as a finding.\n  .exitOverride();\n\n/**\n * Parse a numeric CLI option, refusing what the config schema refuses.\n *\n * `Number.parseFloat`/`parseInt` return NaN for `abc` and silently accept\n * out-of-range values, and NaN then disables whatever gate it feeds — a cost\n * cap that never fires, a confidence gate that writes everything, a `--top`\n * that asks for a negative number of rows. The documented precedence is\n * config → Ajv → CLI override, so the override has to be held to the same range.\n */\nfunction numericOption(\n  flag: string,\n  { min, max, integer }: { min: number; max?: number; integer?: boolean },\n) {\n  return (raw: string): number => {\n    const value = Number.parseFloat(raw);\n    if (!Number.isFinite(value)) {\n      throw new GraphError(`${flag} expects a number, got \"${raw}\".`);\n    }\n    if (integer && !Number.isInteger(value)) {\n      throw new GraphError(`${flag} expects a whole number, got ${value}.`);\n    }\n    if (value < min || (max !== undefined && value > max)) {\n      const range = max === undefined ? `>= ${min}` : `${min}..${max}`;\n      throw new GraphError(`${flag} must be ${range}, got ${value}.`);\n    }\n    return value;\n  };\n}\n\n/** A count: a whole number, at least `min` (1 unless the flag allows zero). */\nfunction countOption(flag: string, min = 1) {\n  return numericOption(flag, { min, integer: true });\n}\n\n/**\n * Hold a CLI override to the same list its config key is held to.\n *\n * `fill.provider` is Ajv-validated against the schema enum; the `--provider`\n * override was an arbitrary string cast straight to `ProviderName`, so the\n * documented config → Ajv → CLI precedence had a hole at the last step.\n */\nfunction enumOption<T extends string>(flag: string, allowed: readonly T[]) {\n  return (raw: string): T => {\n    if (!(allowed as readonly string[]).includes(raw)) {\n      throw new GraphError(\n        `${flag} must be one of ${allowed.join(\" | \")}, got \"${raw}\".`,\n      );\n    }\n    return raw as T;\n  };\n}\n\n/**\n * A flag whose value is one of a named set, refused in the family's words:\n * `Unknown --format \"xml\". Use pretty | json.` The check runs while the\n * options are parsed, so a typo costs a message rather than a graph load.\n */\nfunction choiceOption<T extends string>(flag: string, allowed: readonly T[]) {\n  return (raw: string): T => {\n    if (!(allowed as readonly string[]).includes(raw)) {\n      throw new GraphError(`Unknown ${flag} \"${raw}\". Use ${allowed.join(\" | \")}.`);\n    }\n    return raw as T;\n  };\n}\n\n/** `-f, --format`: every verb's list is `pretty | json` (0051 §2). */\nconst formatOption = choiceOption(\"--format\", GRAPH_FORMATS);\n\n/** `check`'s own, which adds `github` — the CI gate's annotation format. */\nconst checkFormatOption = choiceOption(\"--format\", CHECK_FORMATS);\n\n/**\n * `--fields <list>`: comma-separated and given once, never repeatable — one\n * separator per list (proposal 0034), and the spelling `meta fill --fields`\n * already uses. Each value is held to the same list `fill.fields` is.\n */\nconst fieldsOption = (raw: string): FillField[] =>\n  splitList(raw).map((value) => enumOption(\"--fields\", ALL_FILL_FIELDS)(value));\n\n/**\n * The document-set surface the verbs that read documents share (proposals\n * 0041 and 0051 §1): positional `[paths...]` with `-` for stdin,\n * `--collection` and `--exclude` (each one value per occurrence), `--as`,\n * `--ext` (comma-separated, given once), `--allow-empty`, and\n * `-c`/`--no-config`. Declared once so the verbs cannot drift apart on a name\n * or a description, and worded as `meta` and `lint` word them.\n */\nfunction documentInputs(command: Command, verb: string): Command {\n  return command\n    .argument(\n      \"[paths...]\",\n      `files, directories, or globs to ${verb} (use - for stdin)`,\n    )\n    .option(\n      \"--collection <name>\",\n      \"Configured collection to read (repeatable)\",\n      collect,\n      [],\n    )\n    .option(\"--exclude <glob>\", \"Glob to exclude (repeatable)\", collect, [])\n    .option(\n      \"--as <format>\",\n      \"Parse every input as asciidoc, html, markdown, mdx, rst or xml, whatever its extension. Required with -.\",\n    )\n    .option(\n      \"--ext <list>\",\n      \"comma-separated extensions for directory walks\",\n      DEFAULT_EXTENSIONS.join(\",\"),\n    )\n    .option(\"--allow-empty\", \"treat zero matched files as success\")\n    .option(\"-c, --config <path>\", \"Path to manni.config.yaml\")\n    .option(\"--no-config\", \"Ignore any discovered config file\");\n}\n\n/** The input flags as commander hands them over. */\ninterface InputFlags {\n  as?: string;\n  ext: string;\n  allowEmpty?: boolean;\n}\n\n/**\n * The input flags for a core, and stdin when `paths` holds `-`. `--as` is\n * checked first, so `-` without it is refused before anything waits on stdin.\n */\nasync function inputOptions(\n  paths: string[],\n  opts: InputFlags,\n): Promise<{\n  as?: string;\n  ext: string[];\n  allowEmpty?: boolean;\n  stdinContent?: string;\n}> {\n  assertInputFormat(paths, opts.as);\n  return {\n    ...(opts.as === undefined ? {} : { as: opts.as }),\n    ext: splitList(opts.ext),\n    ...(opts.allowEmpty === true ? { allowEmpty: true } : {}),\n    ...(paths.includes(STDIN) ? { stdinContent: await readStdin() } : {}),\n  };\n}\n\n/**\n * `-c`/`--no-config` for a verb that reads a built graph rather than a\n * document set. They share one commander attribute, which `configOption`\n * splits.\n */\nfunction configInputs(command: Command): Command {\n  return command\n    .option(\"-c, --config <path>\", \"Path to manni.config.yaml\")\n    .option(\"--no-config\", \"Ignore any discovered config file\");\n}\n\n/**\n * `opts` minus the one attribute `-c` and `--no-config` share. `documentOptions`\n * restates it as the two fields a core reads, and spreading the raw value over\n * them would put commander's `false` back where a path belongs.\n */\nfunction rest<T extends { config?: string | boolean }>(\n  opts: T,\n): Omit<T, \"config\"> {\n  const { config, ...others } = opts;\n  return others;\n}\n\n/** The shared options as the command cores take them. */\nfunction documentOptions(opts: {\n  collection?: string[];\n  exclude?: string[];\n  config?: string | boolean;\n}): {\n  config?: string;\n  noConfig?: boolean;\n  collection?: string[];\n  exclude?: string[];\n} {\n  const { configPath, noConfig } = configOption(opts.config);\n  return {\n    ...(configPath === undefined ? {} : { config: configPath }),\n    ...(noConfig === true ? { noConfig } : {}),\n    ...(opts.collection === undefined ? {} : { collection: opts.collection }),\n    ...(opts.exclude === undefined ? {} : { exclude: opts.exclude }),\n  };\n}\n\nprogram\n  .command(\"init\")\n  .description(\"Add a starter `graph:` section to manni.config.yaml in the current directory\")\n  .action(async () => {\n    try {\n      console.log(`Created ${await runInit()}`);\n    } catch (e) {\n      fail(e);\n    }\n  });\n\ndocumentInputs(\n  program\n    .command(\"build\")\n    .description(\"Derive the knowledge graph and write deterministic Turtle\"),\n  \"build\",\n)\n  .option(\"-o, --out <path>\", \"Output .ttl path (default: config out)\")\n  .action(async (paths: string[], opts: InputFlags & {\n    config?: string | boolean;\n    collection?: string[];\n    exclude?: string[];\n    out?: string;\n  }) => {\n    try {\n      const result = await runBuild({\n        paths,\n        ...documentOptions(opts),\n        ...(await inputOptions(paths, opts)),\n        out: opts.out,\n      });\n      // Warnings go to stderr so stdout stays the machine-readable summary;\n      // a degraded build is still a successful one, so the exit code is 0.\n      for (const warning of result.warnings) warn(warning);\n      console.log(\n        `Wrote ${result.outPath} (${result.docs} docs, ${result.quads} triples)`,\n      );\n    } catch (e) {\n      fail(e);\n    }\n  });\n\nconfigInputs(\n  program\n    .command(\"check\")\n    .description(\n      \"Validate the built graph against the bundled SHACL shapes (errors exit 1)\",\n    ),\n)\n  .option(\"-g, --graph <path>\", \"Graph .ttl path (default: config out)\")\n  // One path per occurrence, never split on commas: a path may hold one.\n  .option(\n    \"--shapes <path>\",\n    \"Shapes .ttl file; repeatable (default: config check.shapes, then bundled)\",\n    collect,\n    [],\n  )\n  .option(\n    \"-f, --format <format>\",\n    `Output: ${CHECK_FORMAT_LIST}`,\n    checkFormatOption,\n    \"pretty\",\n  )\n  .action(\n    async (opts: {\n      config?: string | boolean;\n      graph?: string;\n      shapes: string[];\n      format: CheckFormat;\n    }) => {\n      try {\n        const report = await runCheck({ ...rest(opts), ...documentOptions(opts) });\n        console.log(renderCheck(report, opts.format));\n        process.exitCode = report.exitCode;\n      } catch (e) {\n        fail(e);\n      }\n    },\n  );\n\ndocumentInputs(\n  program\n    .command(\"fill\")\n    .description(\n      \"Propose `graph:` frontmatter fields with an LLM, gated by confidence, and write them back\",\n    ),\n  \"fill\",\n)\n  .option(\n    \"-f, --format <format>\",\n    `Output: ${GRAPH_FORMAT_LIST}`,\n    formatOption,\n    \"pretty\",\n  )\n  .option(\"--dry-run\", \"Report proposals without writing files\")\n  .option(\"--force\", \"Overwrite human-set graph fields\")\n  .option(\"--no-cache\", \"Bypass the proposal cache\")\n  .option(\"--no-validate-graph\", \"Skip the SHACL graph guardrail on proposals\")\n  .option(\"--sections\", \"Also propose per-section metadata\")\n  .option(\n    \"--max-turns <n>\",\n    \"Stop after this many inference calls (a cached page costs none)\",\n    countOption(\"--max-turns\"),\n  )\n  .option(\n    \"--confidence <n>\",\n    \"Minimum model confidence (0..1) to write a field (default: config, 0.7)\",\n    numericOption(\"--confidence\", { min: 0, max: 1 }),\n  )\n  .option(\n    // Comma-separated and given once: one separator per list (proposal 0034).\n    \"--fields <list>\",\n    `Fields to propose (comma-separated; default: config, then every field)`,\n    fieldsOption,\n  )\n  // The nameable providers, and `auto`. `mock` is the library's test double:\n  // accepted when asked for by name, never offered.\n  .option(\n    \"--provider <name>\",\n    \"Provider: auto (default) | anthropic | openai | claude-cli | llama-cpp\",\n  )\n  .option(\"--model <model>\", \"Model override; needs a named provider, from here or config\")\n  .option(\"--local\", LOCAL_FLAG_HELP)\n  // Typed inline, as every other action in this file is. The option parsers\n  // above (`numericOption`, `choiceOption`, `fieldsOption`) have already thrown\n  // on anything malformed by the time this runs, so a cast per field would be\n  // safe — but it would also be the one command with the most options and the\n  // least help from the compiler.\n  .action(async (paths: string[], opts: InputFlags & {\n    config?: string | boolean;\n    collection?: string[];\n    exclude?: string[];\n    dryRun?: boolean;\n    force?: boolean;\n    cache?: boolean;\n    validateGraph?: boolean;\n    sections?: boolean;\n    maxTurns?: number;\n    confidence?: number;\n    fields?: FillField[];\n    provider?: string;\n    model?: string;\n    local?: boolean;\n    format: GraphFormat;\n  }) => {\n    try {\n      const report = await runFill({\n        paths,\n        ...documentOptions(opts),\n        ...(await inputOptions(paths, opts)),\n        dryRun: opts.dryRun,\n        force: opts.force,\n        noCache: opts.cache === false,\n        noValidateGraph: opts.validateGraph === false,\n        sections: opts.sections,\n        maxTurns: opts.maxTurns,\n        confidence: opts.confidence,\n        fields: opts.fields,\n        provider: opts.provider,\n        model: opts.model,\n        local: opts.local,\n      });\n      // Same channel discipline as build: warnings on stderr, so stdout stays\n      // the report, and a warning never changes the exit code.\n      for (const warning of report.warnings) warn(warning);\n      const rendered = renderFill(report, opts.format);\n      if (paths.includes(STDIN)) {\n        // With `-` the filled document owns stdout, as under `meta fill -`,\n        // and the report in either format is a diagnostic on stderr.\n        if (report.stdinDocument !== undefined) {\n          process.stdout.write(report.stdinDocument);\n        }\n        if (rendered.length > 0) process.stderr.write(`${rendered}\\n`);\n      } else {\n        console.log(rendered);\n      }\n      process.exitCode = report.exitCode;\n    } catch (e) {\n      fail(e);\n    }\n  });\n\nprogram\n  .command(\"query\")\n  .description(\n    \"Match triple patterns against the built graph (omit a term for wildcard)\",\n  )\n  // Long-only, and named for the triple position each one fills. `-o` is\n  // `--out` on every other graph verb and `-s` is meta's schema flag; a\n  // one-letter spelling that means two things in one family costs more than\n  // the letters it saves.\n  .option(\"--subject <term>\", \"Subject IRI or prefixed name\")\n  .option(\"--predicate <term>\", \"Predicate IRI or prefixed name\")\n  .option(\"--object <term>\", \"Object IRI, prefixed name, or literal value\")\n  .option(\"-c, --config <path>\", \"Path to manni.config.yaml\")\n  .option(\"--no-config\", \"Ignore any discovered config file\")\n  .option(\"-g, --graph <path>\", \"Graph .ttl path (default: config out)\")\n  .option(\n    \"-f, --format <format>\",\n    `Output: ${GRAPH_FORMAT_LIST}`,\n    formatOption,\n    \"pretty\",\n  )\n  .action(\n    (opts: {\n      subject?: string;\n      predicate?: string;\n      object?: string;\n      config?: string | boolean;\n      graph?: string;\n      format: GraphFormat;\n    }) => {\n      try {\n        const { subject, predicate, object, ...others } = rest(opts);\n        const result = runQuery({\n          ...others,\n          ...documentOptions(opts),\n          ...(subject === undefined ? {} : { s: subject }),\n          ...(predicate === undefined ? {} : { p: predicate }),\n          ...(object === undefined ? {} : { o: object }),\n        });\n        console.log(renderQuery(result, opts.format));\n      } catch (e) {\n        fail(e);\n      }\n    },\n  );\n\nprogram\n  .command(\"stats\")\n  .description(\n    \"Summarize the built graph: counts, orphans, broken links, hubs, metadata coverage\",\n  )\n  .option(\"-c, --config <path>\", \"Path to manni.config.yaml\")\n  .option(\"--no-config\", \"Ignore any discovered config file\")\n  .option(\"-g, --graph <path>\", \"Graph .ttl path (default: config out)\")\n  .option(\n    \"-f, --format <format>\",\n    `Output: ${GRAPH_FORMAT_LIST}`,\n    formatOption,\n    \"pretty\",\n  )\n  .option(\n    \"--check\",\n    \"Exit 1 when broken internal links exist or coverage is below threshold\",\n  )\n  .option(\n    \"--top <n>\",\n    \"How many most-connected docs to list\",\n    countOption(\"--top\"),\n  )\n  .option(\n    \"--coverage-threshold <pct>\",\n    \"Minimum metadata coverage % (all fields); overrides config for this run\",\n    // A percentage, so 0..100 rather than the 0..1 of a confidence. NaN here is\n    // worse than a wrong number: `pct < NaN` is false for every field, so the\n    // gate this flag exists to tighten would silently pass instead.\n    numericOption(\"--coverage-threshold\", { min: 0, max: 100 }),\n  )\n  .action(\n    (opts: {\n      config?: string | boolean;\n      graph?: string;\n      format: GraphFormat;\n      check?: boolean;\n      top?: number;\n      coverageThreshold?: number;\n    }) => {\n      try {\n        const report = runStats({ ...rest(opts), ...documentOptions(opts) });\n        console.log(renderStats(report, opts.format));\n        process.exitCode = report.exitCode;\n      } catch (e) {\n        fail(e);\n      }\n    },\n  );\n\nprogram\n  .command(\"search\")\n  .description(\"Rank graph nodes for a text query (needs `export search`)\")\n  .argument(\"<query>\", \"Text query\")\n  .option(\"-c, --config <path>\", \"Path to manni.config.yaml\")\n  .option(\"--no-config\", \"Ignore any discovered config file\")\n  .option(\"-g, --graph <path>\", \"Graph .ttl path (default: config out)\")\n  .option(\n    \"-i, --index <dir>\",\n    \"Directory holding the indexes and manifest (default: beside the graph)\",\n  )\n  .option(\n    \"--lang <tag>\",\n    \"Which localization to search (required when the corpus has more than one)\",\n  )\n  .option(\"--limit <n>\", \"Maximum results (default 10)\", countOption(\"--limit\"))\n  .option(\n    \"--vectors <path>\",\n    \"Vector sidecar path (default: from the manifest)\",\n  )\n  .option(\n    \"--mode <mode>\",\n    `Which legs to run: ${SEARCH_MODES.join(\" | \")} (default: hybrid when vectors exist)`,\n    choiceOption(\"--mode\", SEARCH_MODES),\n  )\n  .option(\n    \"-f, --format <format>\",\n    `Output: ${GRAPH_FORMAT_LIST}`,\n    formatOption,\n    \"pretty\",\n  )\n  .action(\n    async (\n      query: string,\n      opts: {\n        config?: string | boolean;\n        graph?: string;\n        index?: string;\n        lang?: string;\n        limit?: number;\n        vectors?: string;\n        mode?: SearchMode;\n        format: GraphFormat;\n      },\n    ) => {\n      try {\n        const report = await runSearch({\n          ...rest(opts),\n          ...documentOptions(opts),\n          query,\n        });\n        console.log(renderSearch(report, opts.format));\n      } catch (e) {\n        fail(e);\n      }\n    },\n  );\n\nprogram\n  .command(\"traverse\")\n  .description(\n    \"Walk the graph from a node, honoring scope rules, with the full trace\",\n  )\n  .argument(\"<node>\", \"Starting node: a full IRI or a prefix:local CURIE\")\n  .option(\"-c, --config <path>\", \"Path to manni.config.yaml\")\n  .option(\"--no-config\", \"Ignore any discovered config file\")\n  .option(\"-g, --graph <path>\", \"Graph .ttl path (default: config out)\")\n  .option(\n    \"-d, --depth <n>\",\n    \"Maximum hops from the node (default 1; 3 under --impact)\",\n    // Zero is allowed: it means the node itself, which is a real answer.\n    countOption(\"--depth\", 0),\n  )\n  // Comma-separated and given once: a CURIE holds no comma, so one separator\n  // is enough, and a second spelling would be a second thing to document.\n  .option(\n    \"--predicates <list>\",\n    \"Only follow these predicates (comma-separated)\",\n  )\n  .option(\"--reverse\", \"Follow inbound edges (who points at this node)\")\n  .option(\"--impact\", \"Transitive inbound reach: what a change here affects\")\n  .option(\n    \"--variant <variant>\",\n    \"Scope filter: product variant IRI, title, or slug\",\n  )\n  // Not `--subject`: on `query` that is a triple's subject, and one flag name\n  // means one thing across the domain.\n  .option(\"--software-subject <subject>\", \"Scope filter: software subject\")\n  .option(\"--lang <tag>\", \"Scope filter: BCP-47 language tag, matched in any case\")\n  .option(\"--limit <n>\", \"Stop after this many nodes\", countOption(\"--limit\"))\n  .option(\n    \"-f, --format <format>\",\n    `Output: ${GRAPH_FORMAT_LIST}`,\n    formatOption,\n    \"pretty\",\n  )\n  .action(\n    (\n      node: string,\n      opts: {\n        config?: string | boolean;\n        graph?: string;\n        depth?: number;\n        predicates?: string;\n        reverse?: boolean;\n        impact?: boolean;\n        variant?: string;\n        softwareSubject?: string;\n        lang?: string;\n        limit?: number;\n        format: GraphFormat;\n      },\n    ) => {\n      try {\n        const { softwareSubject, ...others } = rest(opts);\n        const report = runTraverse({\n          ...others,\n          ...documentOptions(opts),\n          ...(softwareSubject === undefined ? {} : { subject: softwareSubject }),\n          node,\n          predicates:\n            opts.predicates === undefined\n              ? undefined\n              : splitList(opts.predicates),\n        });\n        console.log(renderTraverse(report, opts.format));\n      } catch (e) {\n        fail(e);\n      }\n    },\n  );\n\nprogram\n  .command(\"embed\")\n  .description(\n    \"Compute local embeddings for the search index (needs @huggingface/transformers)\",\n  )\n  .option(\"-c, --config <path>\", \"Path to manni.config.yaml\")\n  .option(\"--no-config\", \"Ignore any discovered config file\")\n  .option(\"-g, --graph <path>\", \"Graph .ttl path (default: config out)\")\n  .option(\n    \"-i, --index <dir>\",\n    \"Directory holding the indexes and manifest (default: beside the graph)\",\n  )\n  .option(\n    \"-o, --out <dir>\",\n    \"Directory for the sidecars (default: the index directory)\",\n  )\n  // Not `--model`: on `fill` that is the inference model, a different thing.\n  .option(\n    \"--embedding-model <id>\",\n    \"Embedding model id (any id; `mock` for offline runs)\",\n  )\n  .option(\"--dtype <dtype>\", \"Weight quantization (default q8)\")\n  .option(\"--no-cache\", \"Ignore the vector cache\")\n  .option(\n    \"-f, --format <format>\",\n    `Output: ${GRAPH_FORMAT_LIST}`,\n    formatOption,\n    \"pretty\",\n  )\n  .action(\n    async (opts: {\n      config?: string | boolean;\n      graph?: string;\n      index?: string;\n      out?: string;\n      embeddingModel?: string;\n      dtype?: string;\n      cache?: boolean;\n      format: GraphFormat;\n    }) => {\n      try {\n        const { embeddingModel, ...others } = rest(opts);\n        const report = await runEmbed({\n          ...others,\n          ...documentOptions(opts),\n          ...(embeddingModel === undefined ? {} : { model: embeddingModel }),\n          noCache: opts.cache === false,\n        });\n        console.log(renderEmbed(report, opts.format));\n      } catch (e) {\n        fail(e);\n      }\n    },\n  );\n\nprogram\n  .command(\"export\")\n  .description(\n    \"Reserialize the built graph into a consumer format (jsonld file, iirds package, or search index)\",\n  )\n  // The target is a positional, not `-f`: `-f` is the output format in every\n  // other verb of the family (0051 §2), and one flag cannot mean two things.\n  .argument(\"<target>\", `What to write: ${EXPORT_TARGETS.join(\" | \")}`)\n  .option(\"-c, --config <path>\", \"Path to manni.config.yaml\")\n  .option(\"--no-config\", \"Ignore any discovered config file\")\n  .option(\"-g, --graph <path>\", \"Graph .ttl path (default: config out)\")\n  .option(\n    \"-o, --out <path>\",\n    \"Output path (default: the graph path with the target's extension)\",\n  )\n  .action(\n    async (\n      target: string,\n      opts: { config?: string | boolean; graph?: string; out?: string },\n    ) => {\n      try {\n        if (!(EXPORT_TARGETS as readonly string[]).includes(target)) {\n          throw new GraphError(\n            `Unknown export target \"${target}\". Use ${EXPORT_TARGETS.join(\" | \")}.`,\n          );\n        }\n        const result = await runExport({\n          ...documentOptions(opts),\n          graph: opts.graph,\n          format: target as ExportFormat,\n          out: opts.out,\n        });\n        for (const warning of result.warnings) warn(warning);\n        console.log(\n          `Wrote ${result.nodes} node${result.nodes === 1 ? \"\" : \"s\"} to ${result.outPath}`,\n        );\n      } catch (e) {\n        fail(e);\n      }\n    },\n  );\n\nreturn program;\n}\n","/**\n * What `-f` accepts, per verb.\n *\n * Each verb's renderer lives beside its command core (`renderCheck`,\n * `renderStats`, …); what belongs here is the *list*, stated once so the\n * union, the guard, the help text and the refusal sentence cannot drift\n * apart. It is the same shape a11y and cite keep (`A11Y_FORMATS`,\n * `REPORT_FORMATS`), which is why the sentence a user reads is the family's.\n *\n * Every verb takes `pretty | json`. `check` also takes `github`, because it is\n * the CI gate: it is the one graph verb whose output changes what a reviewer sees\n * on a pull request (proposal 0051 §2). It names its own list here rather than\n * widening the shared one, so no other verb advertises a format it cannot\n * render.\n */\n\n/** The list every graph verb's `-f` accepts, in the order messages list them. */\nexport const GRAPH_FORMATS = [\"pretty\", \"json\"] as const;\nexport type GraphFormat = (typeof GRAPH_FORMATS)[number];\n\n/** `\"pretty | json\"`, for help text and the refusal sentence. */\nexport const GRAPH_FORMAT_LIST: string = GRAPH_FORMATS.join(\" | \");\n\n/** `check`'s list: the shared two plus the CI annotation format. */\nexport const CHECK_FORMATS = [...GRAPH_FORMATS, \"github\"] as const;\nexport type CheckFormat = (typeof CHECK_FORMATS)[number];\n\n/** `\"pretty | json | github\"`, for help text and the refusal sentence. */\nexport const CHECK_FORMAT_LIST: string = CHECK_FORMATS.join(\" | \");\n","/**\n * `manni graph init` — scaffold a starter `graph:` section in manni.config.yaml.\n *\n * The family file is shared with the other tools, so a file that already\n * exists is not overwritten: the section is appended to it, leaving the\n * siblings' keys and comments exactly as they were. A file that already has a\n * `graph:` key is refused.\n */\nimport { existsSync, readFileSync } from \"node:fs\";\nimport { resolve } from \"node:path\";\nimport { parse as parseYaml } from \"yaml\";\nimport { errorMessage } from \"../../shared/errors.js\";\nimport { writeTextAtomic } from \"../../shared/write-file.js\";\nimport { GraphError } from \"../types.js\";\nimport { CONFIG_SECTION, DEFAULT_CONFIG_FILENAME } from \"../core/config.js\";\n\nconst HEADER = `# manni.config.yaml — shared configuration for the manni family of tools.\n# Each tool reads its own top-level key; manni graph reads \"graph:\".\n`;\n\nconst STARTER = `# Base IRI for every minted node. Set this to a namespace you control;\n# without it, IRIs fall back to the urn:manni:graph: placeholder.\n# baseIri: https://example.com/graph/\n\n# There is no document set here. \\`manni graph build\\` and \\`manni graph fill\\` read the\n# paths you name, or the collections declared once for every tool at the TOP\n# level of this file, beside \\`graph:\\` rather than inside it:\n#\n#   collections:\n#     - name: site\n#       paths: [\"docs/**/*.md\"]\n#\n# Output of \\`manni graph build\\`.\nout: graph/graph.ttl\n\n# Map published-site routes back to source files so route-style links\n# (/docs/actions/find) become graph edges. A route may also carry the BCP-47\n# \\`language\\` labelling every document under its root; a page's own \\`lang\\`\n# frontmatter wins. Uncomment and adjust:\n# routes:\n#   - basePath: /docs\n#     root: docs\n#     extensions: [.md, .mdx, .markdown]\n#     indexFiles: [index, README]\n#   - basePath: /docs/de\n#     root: docs/de\n#     language: de\n\n# What to derive triples from. Remove entries to opt out.\nbuild:\n  derive: [frontmatter, sections, links, tags, images, code, provenance]\n\n# PROV-O settings. Git history is detected, not switched: per-file dates and\n# author agents, rename -> prov:wasRevisionOf, and the build activity's HEAD\n# committer date are derived wherever git can run over a repository, and a run\n# that cannot says so once and builds the rest. Deterministic per commit;\n# wall-clock time never enters the graph.\n# qualified: emit prov:qualifiedAttribution/qualifiedAssociation nodes\n#   with roles alongside the direct properties.\nprovenance:\n  qualified: true\n\n# Which fields a published graph may carry is read from x-manni-graph-output in\n# the schema set \\`manni meta validate\\` resolves for each page. Set that under\n# meta: (schemas, strict, register), not here. The default set keeps the\n# stewardship people fields (owner, stakeholders, reviewed-by) out.\n\n# SHACL shapes \\`manni graph check\\` validates the built graph against. Default:\n# the shapes contract bundled with manni (shapes/graph/shapes-1.0.0.ttl).\n# check:\n#   shapes: [\"./my-shapes.ttl\"]\n\n# Metadata coverage gate for \\`manni graph stats --check\\`. A number applies to\n# every measured field; a map gates named fields only. Unset gates nothing.\n# stats:\n#   coverageThreshold:\n#     title: 100\n#     description: 50\n\n# Which provider \\`manni graph fill\\` sends pages to. Unset, the family's\n# top-level providers: map decides, and then \\`auto\\`, which detects one: an\n# Anthropic key, then an OpenAI key, then the Claude CLI, then a local model.\n# Connection settings (apiKeyEnv, baseUrl, command) live in that map, declared\n# once for every manni tool. \\`--provider\\` wins over this, \\`--local\\` over both.\n# provider: anthropic          # auto | anthropic | openai | claude-cli | llama-cpp\n# model: claude-sonnet-4-5     # the provider's default when omitted\n\n# LLM settings for \\`manni graph fill\\` (SKOS frontmatter proposals).\nfill:\n  temperature: 0\n  # Stop after this many inference calls. One page is one turn, and a cached\n  # page spends none. Unset is unbounded.\n  # maxTurns: 50\n  cacheDir: .manni/graph/cache\n  # fill proposes every field; confidence (0..1 per field) gates what is\n  # written. Fields scored below the threshold are reported, not written.\n  confidenceThreshold: 0.7\n  # fields: defaults to every fillable field — uncomment to restrict.\n  # Record meta-provenance (model + /graph/ pointers + confidence) on filled docs.\n  writeProvenance: true\n  # Reject proposals that would violate the SHACL shapes contract\n  # (broader/narrower cycles, conflicting labels).\n  validateGraph: true\n  # Also propose per-section metadata. Off by default: it costs more output per\n  # call, and section metadata is explicit-only, so review it as carefully.\n  sections: false\n\n# Local embeddings for semantic search (\\`manni graph embed\\`). Needs the optional\n# peer: npm install @huggingface/transformers\n# embed:\n#   model: onnx-community/granite-embedding-small-english-r2-ONNX\n#   dtype: q8            # q8 keeps embedding reproducible across platforms\n#   out: graph              # directory for the per-language vector sidecars\n#   cacheDir: .manni/graph/embed-cache\n\n# Optional enrichment for \\`manni graph export iirds\\` (the iiRDS package).\n# Absent, a minimal valid package is still produced.\n# export:\n#   iirds:\n#     title: My Docs        # package title (default: \"manni graph export\")\n#     creator: Acme Corp     # Creator iirds:Party + vcard:Organization\n#     version: \"1.3\"         # iiRDS version literal: \"1.2\" | \"1.3\"\n`;\n\n/** The starter as a `graph:` section: every line nested one level. */\nfunction starterSection(): string {\n  const body = STARTER.split(\"\\n\")\n    .map((line) => (line === \"\" ? \"\" : `  ${line}`))\n    .join(\"\\n\");\n  return `${CONFIG_SECTION}:\\n${body}`;\n}\n\nexport async function runInit(cwd = process.cwd()): Promise<string> {\n  const path = resolve(cwd, DEFAULT_CONFIG_FILENAME);\n  if (!existsSync(path)) {\n    await writeTextAtomic(path, `${HEADER}${starterSection()}`);\n    return path;\n  }\n\n  // A family file is already here. Parse it to make sure a `graph:` key can be\n  // appended: the document must be a mapping (or empty) without one.\n  const text = readFileSync(path, \"utf8\");\n  let doc: unknown;\n  try {\n    doc = parseYaml(text);\n  } catch (e) {\n    throw new GraphError(\n      `Invalid YAML in ${DEFAULT_CONFIG_FILENAME}: ${errorMessage(e)}`,\n    );\n  }\n  if (doc != null && (typeof doc !== \"object\" || Array.isArray(doc))) {\n    throw new GraphError(\n      `${DEFAULT_CONFIG_FILENAME}: top level must be a mapping — not adding a \\`${CONFIG_SECTION}:\\` section to it.`,\n    );\n  }\n  if (doc != null && Object.hasOwn(doc, CONFIG_SECTION)) {\n    throw new GraphError(\n      `${DEFAULT_CONFIG_FILENAME} already has a \\`${CONFIG_SECTION}:\\` section — not overwriting.`,\n    );\n  }\n  // Append as text rather than re-serialising the document, so the siblings'\n  // keys and comments come out byte-for-byte as they went in.\n  const separator = text === \"\" || text.endsWith(\"\\n\") ? \"\" : \"\\n\";\n  const blank = text === \"\" ? \"\" : \"\\n\";\n  await writeTextAtomic(\n    path,\n    `${text}${separator}${blank}${starterSection()}`,\n  );\n  return 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+{"version":3,"sources":["../src/graph/cli.ts","../src/graph/reporters/index.ts","../src/graph/commands/init.ts"],"sourcesContent":["/**\n * The graph program. Named `graph` because that is where it is mounted\n * (`manni graph …`); `src/cli.ts` adds it to the umbrella and runs it.\n *\n * Grammar per proposals 0034 and 0051 §2: the domain owns verbs and has no\n * default subcommand, `-f` means the output format everywhere and is checked\n * against the verb's list, and a list reaches a flag by exactly one\n * separator. The plumbing is the family's: `fail()` from `src/shared/run.ts`,\n * `warn()` from `src/shared/warn.ts`, and `--no-color` from\n * `src/shared/color.ts`.\n */\nimport { Command } from \"commander\";\nimport pkg from \"../../package.json\" with { type: \"json\" };\nimport {\n  collect,\n  configOption,\n  readStdin,\n  splitList,\n} from \"../shared/cli-options.js\";\nimport { shouldColor } from \"../shared/color.js\";\nimport { fail } from \"../shared/run.js\";\nimport { warn } from \"../shared/warn.js\";\nimport { GraphError } from \"./types.js\";\nimport { LOCAL_FLAG_HELP } from \"../shared/providers.js\";\nimport { ALL_FILL_FIELDS, type FillField } from \"./core/config.js\";\nimport {\n  assertInputFormat,\n  DEFAULT_EXTENSIONS,\n  STDIN,\n} from \"./core/discover.js\";\nimport {\n  CHECK_FORMATS,\n  CHECK_FORMAT_LIST,\n  GRAPH_FORMATS,\n  GRAPH_FORMAT_LIST,\n  type CheckFormat,\n  type GraphFormat,\n} from \"./reporters/index.js\";\nimport { runBuild } from \"./commands/build.js\";\nimport { renderCheck, runCheck } from \"./commands/check.js\";\nimport {\n  EXPORT_TARGETS,\n  runExport,\n  type ExportFormat,\n} from \"./commands/export.js\";\nimport { renderQuery, runQuery } from \"./commands/query.js\";\nimport { renderFill, runFill } from \"./commands/fill.js\";\nimport { runInit } from \"./commands/init.js\";\nimport { renderEmbed, runEmbed } from \"./commands/embed.js\";\nimport {\n  renderSearch,\n  runSearch,\n  SEARCH_MODES,\n  type SearchMode,\n} from \"./commands/search.js\";\nimport { renderStats, runStats } from \"./commands/stats.js\";\nimport { renderTraverse, runTraverse } from \"./commands/traverse.js\";\n\n/**\n * Whether `command`'s output gets colour: this domain's `--no-color` and\n * `NO_COLOR` turn it off, and otherwise only a TTY turns it on\n * (`shouldColor`). `isTTY` is passed uncoerced: Node leaves it undefined off\n * a terminal, never false, and `shouldColor` reads a missing one as \"not a\n * terminal\".\n *\n * Exported because this is where the decision is testable — a spawned bin is\n * never a TTY. graph's reporters print no colour yet; when one does, it takes\n * the boolean from here rather than consulting the environment itself.\n */\nexport function colorFor(\n  command: Command,\n  isTTY: boolean | undefined,\n  env?: NodeJS.ProcessEnv,\n): boolean {\n  // commander maps --no-color to opts.color === false, on the command that\n  // declares it.\n  const noColor = colorOwner(command).opts().color === false;\n  return shouldColor({ noColor, isTTY, env });\n}\n\n/**\n * The nearest command, this one or an ancestor, that declares `--no-color`:\n * the `graph` program, wherever it is mounted. Not the root: under the umbrella\n * that is `manni`, which has no `--no-color` of its own.\n */\nfunction colorOwner(command: Command): Command {\n  for (let c: Command | null = command; c !== null; c = c.parent) {\n    if (c.options.some((o) => o.long === \"--no-color\")) return c;\n  }\n  return command;\n}\n\nexport function buildProgram(): Command {\nconst program = new Command();\n\nprogram\n  .name(\"graph\")\n  .description(\n    \"Deterministic knowledge graphs derived from documentation frontmatter and formatting.\",\n  )\n  .version(pkg.version)\n  .option(\"--no-color\", \"disable colored output\")\n  // A pointer, not the whole help screen: the message that precedes it\n  // already names the offending flag.\n  .showHelpAfterError(\"(add --help for usage)\")\n  // MUST come before the `.command()` calls below. `copyInheritedSettings`\n  // copies `_exitCallback` by value at subcommand-creation time, so an\n  // `exitOverride()` installed afterwards leaves every subcommand still\n  // calling `process.exit(1)` — which reports a usage error as a finding.\n  .exitOverride();\n\n/**\n * Parse a numeric CLI option, refusing what the config schema refuses.\n *\n * `Number.parseFloat`/`parseInt` return NaN for `abc` and silently accept\n * out-of-range values, and NaN then disables whatever gate it feeds — a cost\n * cap that never fires, a confidence gate that writes everything, a `--top`\n * that asks for a negative number of rows. The documented precedence is\n * config → Ajv → CLI override, so the override has to be held to the same range.\n */\nfunction numericOption(\n  flag: string,\n  { min, max, integer }: { min: number; max?: number; integer?: boolean },\n) {\n  return (raw: string): number => {\n    const value = Number.parseFloat(raw);\n    if (!Number.isFinite(value)) {\n      throw new GraphError(`${flag} expects a number, got \"${raw}\".`);\n    }\n    if (integer && !Number.isInteger(value)) {\n      throw new GraphError(`${flag} expects a whole number, got ${value}.`);\n    }\n    if (value < min || (max !== undefined && value > max)) {\n      const range = max === undefined ? `>= ${min}` : `${min}..${max}`;\n      throw new GraphError(`${flag} must be ${range}, got ${value}.`);\n    }\n    return value;\n  };\n}\n\n/** A count: a whole number, at least `min` (1 unless the flag allows zero). */\nfunction countOption(flag: string, min = 1) {\n  return numericOption(flag, { min, integer: true });\n}\n\n/**\n * Hold a CLI override to the same list its config key is held to.\n *\n * `fill.provider` is Ajv-validated against the schema enum; the `--provider`\n * override was an arbitrary string cast straight to `ProviderName`, so the\n * documented config → Ajv → CLI precedence had a hole at the last step.\n */\nfunction enumOption<T extends string>(flag: string, allowed: readonly T[]) {\n  return (raw: string): T => {\n    if (!(allowed as readonly string[]).includes(raw)) {\n      throw new GraphError(\n        `${flag} must be one of ${allowed.join(\" | \")}, got \"${raw}\".`,\n      );\n    }\n    return raw as T;\n  };\n}\n\n/**\n * A flag whose value is one of a named set, refused in the family's words:\n * `Unknown --format \"xml\". Use pretty | json.` The check runs while the\n * options are parsed, so a typo costs a message rather than a graph load.\n */\nfunction choiceOption<T extends string>(flag: string, allowed: readonly T[]) {\n  return (raw: string): T => {\n    if (!(allowed as readonly string[]).includes(raw)) {\n      throw new GraphError(`Unknown ${flag} \"${raw}\". Use ${allowed.join(\" | \")}.`);\n    }\n    return raw as T;\n  };\n}\n\n/** `-f, --format`: every verb's list is `pretty | json` (0051 §2). */\nconst formatOption = choiceOption(\"--format\", GRAPH_FORMATS);\n\n/** `check`'s own, which adds `github` — the CI gate's annotation format. */\nconst checkFormatOption = choiceOption(\"--format\", CHECK_FORMATS);\n\n/**\n * `--fields <list>`: comma-separated and given once, never repeatable — one\n * separator per list (proposal 0034), and the spelling `meta fill --fields`\n * already uses. Each value is held to the same list `fill.fields` is.\n */\nconst fieldsOption = (raw: string): FillField[] =>\n  splitList(raw).map((value) => enumOption(\"--fields\", ALL_FILL_FIELDS)(value));\n\n/**\n * The document-set surface the verbs that read documents share (proposals\n * 0041 and 0051 §1): positional `[paths...]` with `-` for stdin,\n * `--collection` and `--exclude` (each one value per occurrence), `--as`,\n * `--ext` (comma-separated, given once), `--allow-empty`, and\n * `-c`/`--no-config`. Declared once so the verbs cannot drift apart on a name\n * or a description, and worded as `meta` and `lint` word them.\n */\nfunction documentInputs(command: Command, verb: string): Command {\n  return command\n    .argument(\n      \"[paths...]\",\n      `files, directories, or globs to ${verb} (use - for stdin)`,\n    )\n    .option(\n      \"--collection <name>\",\n      \"Configured collection to read (repeatable)\",\n      collect,\n      [],\n    )\n    .option(\"--exclude <glob>\", \"Glob to exclude (repeatable)\", collect, [])\n    .option(\n      \"--as <format>\",\n      \"Parse every input as asciidoc, html, markdown, mdx, rst or xml, whatever its extension. Required with -.\",\n    )\n    .option(\n      \"--ext <list>\",\n      \"comma-separated extensions for directory walks\",\n      DEFAULT_EXTENSIONS.join(\",\"),\n    )\n    .option(\"--allow-empty\", \"treat zero matched files as success\")\n    .option(\"-c, --config <path>\", \"Path to manni.config.yaml\")\n    .option(\"--no-config\", \"Ignore any discovered config file\");\n}\n\n/** The input flags as commander hands them over. */\ninterface InputFlags {\n  as?: string;\n  ext: string;\n  allowEmpty?: boolean;\n}\n\n/**\n * The input flags for a core, and stdin when `paths` holds `-`. `--as` is\n * checked first, so `-` without it is refused before anything waits on stdin.\n */\nasync function inputOptions(\n  paths: string[],\n  opts: InputFlags,\n): Promise<{\n  as?: string;\n  ext: string[];\n  allowEmpty?: boolean;\n  stdinContent?: string;\n}> {\n  assertInputFormat(paths, opts.as);\n  return {\n    ...(opts.as === undefined ? {} : { as: opts.as }),\n    ext: splitList(opts.ext),\n    ...(opts.allowEmpty === true ? { allowEmpty: true } : {}),\n    ...(paths.includes(STDIN) ? { stdinContent: await readStdin() } : {}),\n  };\n}\n\n/**\n * `-c`/`--no-config` for a verb that reads a built graph rather than a\n * document set. They share one commander attribute, which `configOption`\n * splits.\n */\nfunction configInputs(command: Command): Command {\n  return command\n    .option(\"-c, --config <path>\", \"Path to manni.config.yaml\")\n    .option(\"--no-config\", \"Ignore any discovered config file\");\n}\n\n/**\n * `opts` minus the one attribute `-c` and `--no-config` share. `documentOptions`\n * restates it as the two fields a core reads, and spreading the raw value over\n * them would put commander's `false` back where a path belongs.\n */\nfunction rest<T extends { config?: string | boolean }>(\n  opts: T,\n): Omit<T, \"config\"> {\n  const { config, ...others } = opts;\n  return others;\n}\n\n/** The shared options as the command cores take them. */\nfunction documentOptions(opts: {\n  collection?: string[];\n  exclude?: string[];\n  config?: string | boolean;\n}): {\n  config?: string;\n  noConfig?: boolean;\n  collection?: string[];\n  exclude?: string[];\n} {\n  const { configPath, noConfig } = configOption(opts.config);\n  return {\n    ...(configPath === undefined ? {} : { config: configPath }),\n    ...(noConfig === true ? { noConfig } : {}),\n    ...(opts.collection === undefined ? {} : { collection: opts.collection }),\n    ...(opts.exclude === undefined ? {} : { exclude: opts.exclude }),\n  };\n}\n\nprogram\n  .command(\"init\")\n  .description(\"Add a starter `graph:` section to manni.config.yaml in the current directory\")\n  .action(async () => {\n    try {\n      console.log(`Created ${await runInit()}`);\n    } catch (e) {\n      fail(e);\n    }\n  });\n\ndocumentInputs(\n  program\n    .command(\"build\")\n    .description(\"Derive the knowledge graph and write deterministic Turtle\"),\n  \"build\",\n)\n  .option(\"-o, --out <path>\", \"Output .ttl path (default: config out)\")\n  .action(async (paths: string[], opts: InputFlags & {\n    config?: string | boolean;\n    collection?: string[];\n    exclude?: string[];\n    out?: string;\n  }) => {\n    try {\n      const result = await runBuild({\n        paths,\n        ...documentOptions(opts),\n        ...(await inputOptions(paths, opts)),\n        out: opts.out,\n      });\n      // Warnings go to stderr so stdout stays the machine-readable summary;\n      // a degraded build is still a successful one, so the exit code is 0.\n      for (const warning of result.warnings) warn(warning);\n      console.log(\n        `Wrote ${result.outPath} (${result.docs} docs, ${result.quads} triples)`,\n      );\n    } catch (e) {\n      fail(e);\n    }\n  });\n\nconfigInputs(\n  program\n    .command(\"check\")\n    .description(\n      \"Validate the built graph against the bundled SHACL shapes (errors exit 1)\",\n    ),\n)\n  .option(\"-g, --graph <path>\", \"Graph .ttl path (default: config out)\")\n  // One path per occurrence, never split on commas: a path may hold one.\n  .option(\n    \"--shapes <path>\",\n    \"Shapes .ttl file; repeatable (default: config check.shapes, then bundled)\",\n    collect,\n    [],\n  )\n  .option(\n    \"-f, --format <format>\",\n    `Output: ${CHECK_FORMAT_LIST}`,\n    checkFormatOption,\n    \"pretty\",\n  )\n  .action(\n    async (opts: {\n      config?: string | boolean;\n      graph?: string;\n      shapes: string[];\n      format: CheckFormat;\n    }) => {\n      try {\n        const report = await runCheck({ ...rest(opts), ...documentOptions(opts) });\n        console.log(renderCheck(report, opts.format));\n        process.exitCode = report.exitCode;\n      } catch (e) {\n        fail(e);\n      }\n    },\n  );\n\ndocumentInputs(\n  program\n    .command(\"fill\")\n    .description(\n      \"Propose `graph:` frontmatter fields with an LLM, gated by confidence, and write them back\",\n    ),\n  \"fill\",\n)\n  .option(\n    \"-f, --format <format>\",\n    `Output: ${GRAPH_FORMAT_LIST}`,\n    formatOption,\n    \"pretty\",\n  )\n  .option(\"--dry-run\", \"Report proposals without writing files\")\n  .option(\"--force\", \"Overwrite human-set graph fields\")\n  .option(\"--no-cache\", \"Bypass the proposal cache\")\n  .option(\"--no-validate-graph\", \"Skip the SHACL graph guardrail on proposals\")\n  .option(\"--sections\", \"Also propose per-section metadata\")\n  .option(\n    \"--max-turns <n>\",\n    \"Stop after this many inference calls (a cached page costs none)\",\n    countOption(\"--max-turns\"),\n  )\n  .option(\n    \"--confidence <n>\",\n    \"Minimum model confidence (0..1) to write a field (default: config, 0.7)\",\n    numericOption(\"--confidence\", { min: 0, max: 1 }),\n  )\n  .option(\n    // Comma-separated and given once: one separator per list (proposal 0034).\n    \"--fields <list>\",\n    `Fields to propose (comma-separated; default: config, then every field)`,\n    fieldsOption,\n  )\n  // The nameable providers, and `auto`. `mock` is the library's test double:\n  // accepted when asked for by name, never offered.\n  .option(\n    \"--provider <name>\",\n    \"Provider: auto (default) | anthropic | openai | claude-cli | llama-cpp\",\n  )\n  .option(\"--model <model>\", \"Model override; needs a named provider, from here or config\")\n  .option(\"--local\", LOCAL_FLAG_HELP)\n  // Typed inline, as every other action in this file is. The option parsers\n  // above (`numericOption`, `choiceOption`, `fieldsOption`) have already thrown\n  // on anything malformed by the time this runs, so a cast per field would be\n  // safe — but it would also be the one command with the most options and the\n  // least help from the compiler.\n  .action(async (paths: string[], opts: InputFlags & {\n    config?: string | boolean;\n    collection?: string[];\n    exclude?: string[];\n    dryRun?: boolean;\n    force?: boolean;\n    cache?: boolean;\n    validateGraph?: boolean;\n    sections?: boolean;\n    maxTurns?: number;\n    confidence?: number;\n    fields?: FillField[];\n    provider?: string;\n    model?: string;\n    local?: boolean;\n    format: GraphFormat;\n  }) => {\n    try {\n      const report = await runFill({\n        paths,\n        ...documentOptions(opts),\n        ...(await inputOptions(paths, opts)),\n        dryRun: opts.dryRun,\n        force: opts.force,\n        noCache: opts.cache === false,\n        noValidateGraph: opts.validateGraph === false,\n        sections: opts.sections,\n        maxTurns: opts.maxTurns,\n        confidence: opts.confidence,\n        fields: opts.fields,\n        provider: opts.provider,\n        model: opts.model,\n        local: opts.local,\n      });\n      // Same channel discipline as build: warnings on stderr, so stdout stays\n      // the report, and a warning never changes the exit code.\n      for (const warning of report.warnings) warn(warning);\n      const rendered = renderFill(report, opts.format);\n      if (paths.includes(STDIN)) {\n        // With `-` the filled document owns stdout, as under `meta fill -`,\n        // and the report in either format is a diagnostic on stderr.\n        if (report.stdinDocument !== undefined) {\n          process.stdout.write(report.stdinDocument);\n        }\n        if (rendered.length > 0) process.stderr.write(`${rendered}\\n`);\n      } else {\n        console.log(rendered);\n      }\n      process.exitCode = report.exitCode;\n    } catch (e) {\n      fail(e);\n    }\n  });\n\nprogram\n  .command(\"query\")\n  .description(\n    \"Match triple patterns against the built graph (omit a term for wildcard)\",\n  )\n  // Long-only, and named for the triple position each one fills. `-o` is\n  // `--out` on every other graph verb and `-s` is meta's schema flag; a\n  // one-letter spelling that means two things in one family costs more than\n  // the letters it saves.\n  .option(\"--subject <term>\", \"Subject IRI or prefixed name\")\n  .option(\"--predicate <term>\", \"Predicate IRI or prefixed name\")\n  .option(\"--object <term>\", \"Object IRI, prefixed name, or literal value\")\n  .option(\"-c, --config <path>\", \"Path to manni.config.yaml\")\n  .option(\"--no-config\", \"Ignore any discovered config file\")\n  .option(\"-g, --graph <path>\", \"Graph .ttl path (default: config out)\")\n  .option(\n    \"-f, --format <format>\",\n    `Output: ${GRAPH_FORMAT_LIST}`,\n    formatOption,\n    \"pretty\",\n  )\n  .action(\n    (opts: {\n      subject?: string;\n      predicate?: string;\n      object?: string;\n      config?: string | boolean;\n      graph?: string;\n      format: GraphFormat;\n    }) => {\n      try {\n        const { subject, predicate, object, ...others } = rest(opts);\n        const result = runQuery({\n          ...others,\n          ...documentOptions(opts),\n          ...(subject === undefined ? {} : { s: subject }),\n          ...(predicate === undefined ? {} : { p: predicate }),\n          ...(object === undefined ? {} : { o: object }),\n        });\n        console.log(renderQuery(result, opts.format));\n      } catch (e) {\n        fail(e);\n      }\n    },\n  );\n\nprogram\n  .command(\"stats\")\n  .description(\n    \"Summarize the built graph: counts, orphans, broken links, hubs, metadata coverage\",\n  )\n  .option(\"-c, --config <path>\", \"Path to manni.config.yaml\")\n  .option(\"--no-config\", \"Ignore any discovered config file\")\n  .option(\"-g, --graph <path>\", \"Graph .ttl path (default: config out)\")\n  .option(\n    \"-f, --format <format>\",\n    `Output: ${GRAPH_FORMAT_LIST}`,\n    formatOption,\n    \"pretty\",\n  )\n  .option(\n    \"--check\",\n    \"Exit 1 when broken internal links exist or coverage is below threshold\",\n  )\n  .option(\n    \"--top <n>\",\n    \"How many most-connected docs to list\",\n    countOption(\"--top\"),\n  )\n  .option(\n    \"--coverage-threshold <pct>\",\n    \"Minimum metadata coverage % (all fields); overrides config for this run\",\n    // A percentage, so 0..100 rather than the 0..1 of a confidence. NaN here is\n    // worse than a wrong number: `pct < NaN` is false for every field, so the\n    // gate this flag exists to tighten would silently pass instead.\n    numericOption(\"--coverage-threshold\", { min: 0, max: 100 }),\n  )\n  .action(\n    (opts: {\n      config?: string | boolean;\n      graph?: string;\n      format: GraphFormat;\n      check?: boolean;\n      top?: number;\n      coverageThreshold?: number;\n    }) => {\n      try {\n        const report = runStats({ ...rest(opts), ...documentOptions(opts) });\n        console.log(renderStats(report, opts.format));\n        process.exitCode = report.exitCode;\n      } catch (e) {\n        fail(e);\n      }\n    },\n  );\n\nprogram\n  .command(\"search\")\n  .description(\"Rank graph nodes for a text query (needs `export search`)\")\n  .argument(\"<query>\", \"Text query\")\n  .option(\"-c, --config <path>\", \"Path to manni.config.yaml\")\n  .option(\"--no-config\", \"Ignore any discovered config file\")\n  .option(\"-g, --graph <path>\", \"Graph .ttl path (default: config out)\")\n  .option(\n    \"-i, --index <dir>\",\n    \"Directory holding the indexes and manifest (default: beside the graph)\",\n  )\n  .option(\n    \"--lang <tag>\",\n    \"Which localization to search (required when the corpus has more than one)\",\n  )\n  .option(\"--limit <n>\", \"Maximum results (default 10)\", countOption(\"--limit\"))\n  .option(\n    \"--vectors <path>\",\n    \"Vector sidecar path (default: from the manifest)\",\n  )\n  .option(\n    \"--mode <mode>\",\n    `Which legs to run: ${SEARCH_MODES.join(\" | \")} (default: hybrid when vectors exist)`,\n    choiceOption(\"--mode\", SEARCH_MODES),\n  )\n  .option(\n    \"-f, --format <format>\",\n    `Output: ${GRAPH_FORMAT_LIST}`,\n    formatOption,\n    \"pretty\",\n  )\n  .action(\n    async (\n      query: string,\n      opts: {\n        config?: string | boolean;\n        graph?: string;\n        index?: string;\n        lang?: string;\n        limit?: number;\n        vectors?: string;\n        mode?: SearchMode;\n        format: GraphFormat;\n      },\n    ) => {\n      try {\n        const report = await runSearch({\n          ...rest(opts),\n          ...documentOptions(opts),\n          query,\n        });\n        console.log(renderSearch(report, opts.format));\n      } catch (e) {\n        fail(e);\n      }\n    },\n  );\n\nprogram\n  .command(\"traverse\")\n  .description(\n    \"Walk the graph from a node, honoring scope rules, with the full trace\",\n  )\n  .argument(\"<node>\", \"Starting node: a full IRI or a prefix:local CURIE\")\n  .option(\"-c, --config <path>\", \"Path to manni.config.yaml\")\n  .option(\"--no-config\", \"Ignore any discovered config file\")\n  .option(\"-g, --graph <path>\", \"Graph .ttl path (default: config out)\")\n  .option(\n    \"-d, --depth <n>\",\n    \"Maximum hops from the node (default 1; 3 under --impact)\",\n    // Zero is allowed: it means the node itself, which is a real answer.\n    countOption(\"--depth\", 0),\n  )\n  // Comma-separated and given once: a CURIE holds no comma, so one separator\n  // is enough, and a second spelling would be a second thing to document.\n  .option(\n    \"--predicates <list>\",\n    \"Only follow these predicates (comma-separated)\",\n  )\n  .option(\"--reverse\", \"Follow inbound edges (who points at this node)\")\n  .option(\"--impact\", \"Transitive inbound reach: what a change here affects\")\n  .option(\n    \"--variant <variant>\",\n    \"Scope filter: product variant IRI, title, or slug\",\n  )\n  // Not `--subject`: on `query` that is a triple's subject, and one flag name\n  // means one thing across the domain.\n  .option(\"--software-subject <subject>\", \"Scope filter: software subject\")\n  .option(\"--lang <tag>\", \"Scope filter: BCP-47 language tag, matched in any case\")\n  .option(\"--limit <n>\", \"Stop after this many nodes\", countOption(\"--limit\"))\n  .option(\n    \"-f, --format <format>\",\n    `Output: ${GRAPH_FORMAT_LIST}`,\n    formatOption,\n    \"pretty\",\n  )\n  .action(\n    (\n      node: string,\n      opts: {\n        config?: string | boolean;\n        graph?: string;\n        depth?: number;\n        predicates?: string;\n        reverse?: boolean;\n        impact?: boolean;\n        variant?: string;\n        softwareSubject?: string;\n        lang?: string;\n        limit?: number;\n        format: GraphFormat;\n      },\n    ) => {\n      try {\n        const { softwareSubject, ...others } = rest(opts);\n        const report = runTraverse({\n          ...others,\n          ...documentOptions(opts),\n          ...(softwareSubject === undefined ? {} : { subject: softwareSubject }),\n          node,\n          predicates:\n            opts.predicates === undefined\n              ? undefined\n              : splitList(opts.predicates),\n        });\n        console.log(renderTraverse(report, opts.format));\n      } catch (e) {\n        fail(e);\n      }\n    },\n  );\n\nprogram\n  .command(\"embed\")\n  .description(\n    \"Compute local embeddings for the search index (needs @huggingface/transformers)\",\n  )\n  .option(\"-c, --config <path>\", \"Path to manni.config.yaml\")\n  .option(\"--no-config\", \"Ignore any discovered config file\")\n  .option(\"-g, --graph <path>\", \"Graph .ttl path (default: config out)\")\n  .option(\n    \"-i, --index <dir>\",\n    \"Directory holding the indexes and manifest (default: beside the graph)\",\n  )\n  .option(\n    \"-o, --out <dir>\",\n    \"Directory for the sidecars (default: the index directory)\",\n  )\n  // Not `--model`: on `fill` that is the inference model, a different thing.\n  .option(\n    \"--embedding-model <id>\",\n    \"Embedding model id (any id; `mock` for offline runs)\",\n  )\n  .option(\"--dtype <dtype>\", \"Weight quantization (default q8)\")\n  .option(\"--no-cache\", \"Ignore the vector cache\")\n  .option(\n    \"-f, --format <format>\",\n    `Output: ${GRAPH_FORMAT_LIST}`,\n    formatOption,\n    \"pretty\",\n  )\n  .action(\n    async (opts: {\n      config?: string | boolean;\n      graph?: string;\n      index?: string;\n      out?: string;\n      embeddingModel?: string;\n      dtype?: string;\n      cache?: boolean;\n      format: GraphFormat;\n    }) => {\n      try {\n        const { embeddingModel, ...others } = rest(opts);\n        const report = await runEmbed({\n          ...others,\n          ...documentOptions(opts),\n          ...(embeddingModel === undefined ? {} : { model: embeddingModel }),\n          noCache: opts.cache === false,\n        });\n        console.log(renderEmbed(report, opts.format));\n      } catch (e) {\n        fail(e);\n      }\n    },\n  );\n\nprogram\n  .command(\"export\")\n  .description(\n    \"Reserialize the built graph into a consumer format (jsonld file, iirds package, or search index)\",\n  )\n  // The target is a positional, not `-f`: `-f` is the output format in every\n  // other verb of the family (0051 §2), and one flag cannot mean two things.\n  .argument(\"<target>\", `What to write: ${EXPORT_TARGETS.join(\" | \")}`)\n  .option(\"-c, --config <path>\", \"Path to manni.config.yaml\")\n  .option(\"--no-config\", \"Ignore any discovered config file\")\n  .option(\"-g, --graph <path>\", \"Graph .ttl path (default: config out)\")\n  .option(\n    \"-o, --out <path>\",\n    \"Output path (default: the graph path with the target's extension)\",\n  )\n  .action(\n    async (\n      target: string,\n      opts: { config?: string | boolean; graph?: string; out?: string },\n    ) => {\n      try {\n        if (!(EXPORT_TARGETS as readonly string[]).includes(target)) {\n          throw new GraphError(\n            `Unknown export target \"${target}\". Use ${EXPORT_TARGETS.join(\" | \")}.`,\n          );\n        }\n        const result = await runExport({\n          ...documentOptions(opts),\n          graph: opts.graph,\n          format: target as ExportFormat,\n          out: opts.out,\n        });\n        for (const warning of result.warnings) warn(warning);\n        console.log(\n          `Wrote ${result.nodes} node${result.nodes === 1 ? \"\" : \"s\"} to ${result.outPath}`,\n        );\n      } catch (e) {\n        fail(e);\n      }\n    },\n  );\n\nreturn program;\n}\n","/**\n * What `-f` accepts, per verb.\n *\n * Each verb's renderer lives beside its command core (`renderCheck`,\n * `renderStats`, …); what belongs here is the *list*, stated once so the\n * union, the guard, the help text and the refusal sentence cannot drift\n * apart. It is the same shape a11y and cite keep (`A11Y_FORMATS`,\n * `REPORT_FORMATS`), which is why the sentence a user reads is the family's.\n *\n * Every verb takes `pretty | json`. `check` also takes `github`, because it is\n * the CI gate: it is the one graph verb whose output changes what a reviewer sees\n * on a pull request (proposal 0051 §2). It names its own list here rather than\n * widening the shared one, so no other verb advertises a format it cannot\n * render.\n */\n\n/** The list every graph verb's `-f` accepts, in the order messages list them. */\nexport const GRAPH_FORMATS = [\"pretty\", \"json\"] as const;\nexport type GraphFormat = (typeof GRAPH_FORMATS)[number];\n\n/** `\"pretty | json\"`, for help text and the refusal sentence. */\nexport const GRAPH_FORMAT_LIST: string = GRAPH_FORMATS.join(\" | \");\n\n/** `check`'s list: the shared two plus the CI annotation format. */\nexport const CHECK_FORMATS = [...GRAPH_FORMATS, \"github\"] as const;\nexport type CheckFormat = (typeof CHECK_FORMATS)[number];\n\n/** `\"pretty | json | github\"`, for help text and the refusal sentence. */\nexport const CHECK_FORMAT_LIST: string = CHECK_FORMATS.join(\" | \");\n","/**\n * `manni graph init` — scaffold a starter `graph:` section in manni.config.yaml.\n *\n * The family file is shared with the other tools, so a file that already\n * exists is not overwritten: the section is appended to it, leaving the\n * siblings' keys and comments exactly as they were. A file that already has a\n * `graph:` key is refused.\n */\nimport { existsSync, readFileSync } from \"node:fs\";\nimport { resolve } from \"node:path\";\nimport { parse as parseYaml } from \"yaml\";\nimport { errorMessage } from \"../../shared/errors.js\";\nimport { writeTextAtomic } from \"../../shared/write-file.js\";\nimport { GraphError } from \"../types.js\";\nimport { CONFIG_SECTION, DEFAULT_CONFIG_FILENAME } from \"../core/config.js\";\n\nconst HEADER = `# manni.config.yaml — shared configuration for the manni family of tools.\n# Each tool reads its own top-level key; manni graph reads \"graph:\".\n`;\n\nconst STARTER = `# Base IRI for every minted node. Set this to a namespace you control;\n# without it, IRIs fall back to the urn:manni:graph: placeholder.\n# baseIri: https://example.com/graph/\n\n# There is no document set here. \\`manni graph build\\` and \\`manni graph fill\\` read the\n# paths you name, or the collections declared once for every tool at the TOP\n# level of this file, beside \\`graph:\\` rather than inside it:\n#\n#   collections:\n#     - name: site\n#       paths: [\"docs/**/*.md\"]\n#\n# Output of \\`manni graph build\\`.\nout: graph/graph.ttl\n\n# Map published-site routes back to source files so route-style links\n# (/docs/actions/find) become graph edges. A route may also carry the BCP-47\n# \\`language\\` labelling every document under its root; a page's own \\`lang\\`\n# frontmatter wins. Uncomment and adjust:\n# routes:\n#   - basePath: /docs\n#     root: docs\n#     extensions: [.md, .mdx, .markdown]\n#     indexFiles: [index, README]\n#   - basePath: /docs/de\n#     root: docs/de\n#     language: de\n\n# What to derive triples from. Remove entries to opt out.\nbuild:\n  derive: [frontmatter, sections, links, tags, images, code, provenance]\n\n# PROV-O settings. Git history is detected, not switched: per-file dates and\n# author agents, rename -> prov:wasRevisionOf, and the build activity's HEAD\n# committer date are derived wherever git can run over a repository, and a run\n# that cannot says so once and builds the rest. Deterministic per commit;\n# wall-clock time never enters the graph.\n# qualified: emit prov:qualifiedAttribution/qualifiedAssociation nodes\n#   with roles alongside the direct properties.\nprovenance:\n  qualified: true\n\n# Which fields a published graph may carry is read from x-manni-graph-output in\n# the schema set \\`manni meta validate\\` resolves for each page. Set that under\n# meta: (schemas, strict, register), not here. The default set keeps the\n# stewardship people fields (owner, stakeholders, reviewed-by) out.\n\n# SHACL shapes \\`manni graph check\\` validates the built graph against. Default:\n# the shapes contract bundled with manni (shapes/graph/shapes-1.0.0.ttl).\n# check:\n#   shapes: [\"./my-shapes.ttl\"]\n\n# Metadata coverage gate for \\`manni graph stats --check\\`. A number applies to\n# every measured field; a map gates named fields only. Unset gates nothing.\n# stats:\n#   coverageThreshold:\n#     title: 100\n#     description: 50\n\n# Which provider \\`manni graph fill\\` sends pages to. Unset, the family's\n# top-level providers: map decides, and then \\`auto\\`, which detects one: an\n# Anthropic key, then an OpenAI key, then the Claude CLI, then a local model.\n# Connection settings (apiKeyEnv, baseUrl, command) live in that map, declared\n# once for every manni tool. \\`--provider\\` wins over this, \\`--local\\` over both.\n# provider: anthropic          # auto | anthropic | openai | claude-cli | llama-cpp\n# model: claude-sonnet-4-5     # the provider's default when omitted\n\n# LLM settings for \\`manni graph fill\\` (SKOS frontmatter proposals).\nfill:\n  temperature: 0\n  # Stop after this many inference calls. One page is one turn, and a cached\n  # page spends none. Unset is unbounded.\n  # maxTurns: 50\n  cacheDir: .manni/graph/cache\n  # fill proposes every field; confidence (0..1 per field) gates what is\n  # written. Fields scored below the threshold are reported, not written.\n  confidenceThreshold: 0.7\n  # fields: defaults to every fillable field — uncomment to restrict.\n  # Record meta-provenance (model + /graph/ pointers + confidence) on filled docs.\n  writeProvenance: true\n  # Reject proposals that would violate the SHACL shapes contract\n  # (broader/narrower cycles, conflicting labels).\n  validateGraph: true\n  # Also propose per-section metadata. Off by default: it costs more output per\n  # call, and section metadata is explicit-only, so review it as carefully.\n  sections: false\n\n# Local embeddings for semantic search (\\`manni graph embed\\`). Needs the optional\n# peer: npm install @huggingface/transformers\n# embed:\n#   model: onnx-community/granite-embedding-small-english-r2-ONNX\n#   dtype: q8            # q8 keeps embedding reproducible across platforms\n#   out: graph              # directory for the per-language vector sidecars\n#   cacheDir: .manni/graph/embed-cache\n\n# Optional enrichment for \\`manni graph export iirds\\` (the iiRDS package).\n# Absent, a minimal valid package is still produced.\n# export:\n#   iirds:\n#     title: My Docs        # package title (default: \"manni graph export\")\n#     creator: Acme Corp     # Creator iirds:Party + vcard:Organization\n#     version: \"1.3\"         # iiRDS version literal: \"1.2\" | \"1.3\"\n`;\n\n/** The starter as a `graph:` section: every line nested one level. */\nfunction starterSection(): string {\n  const body = STARTER.split(\"\\n\")\n    .map((line) => (line === \"\" ? \"\" : `  ${line}`))\n    .join(\"\\n\");\n  return `${CONFIG_SECTION}:\\n${body}`;\n}\n\nexport async function runInit(cwd = process.cwd()): Promise<string> {\n  const path = resolve(cwd, DEFAULT_CONFIG_FILENAME);\n  if (!existsSync(path)) {\n    await writeTextAtomic(path, `${HEADER}${starterSection()}`);\n    return path;\n  }\n\n  // A family file is already here. Parse it to make sure a `graph:` key can be\n  // appended: the document must be a mapping (or empty) without one.\n  const text = readFileSync(path, \"utf8\");\n  let doc: unknown;\n  try {\n    doc = parseYaml(text);\n  } catch (e) {\n    throw new GraphError(\n      `Invalid YAML in ${DEFAULT_CONFIG_FILENAME}: ${errorMessage(e)}`,\n    );\n  }\n  if (doc != null && (typeof doc !== \"object\" || Array.isArray(doc))) {\n    throw new GraphError(\n      `${DEFAULT_CONFIG_FILENAME}: top level must be a mapping — not adding a \\`${CONFIG_SECTION}:\\` section to it.`,\n    );\n  }\n  if (doc != null && Object.hasOwn(doc, CONFIG_SECTION)) {\n    throw new GraphError(\n      `${DEFAULT_CONFIG_FILENAME} already has a \\`${CONFIG_SECTION}:\\` section — not overwriting.`,\n    );\n  }\n  // Append as text rather than re-serialising the document, so the siblings'\n  // keys and comments come out byte-for-byte as they went in.\n  const separator = text === \"\" || text.endsWith(\"\\n\") ? \"\" : \"\\n\";\n  const blank = text === \"\" ? \"\" : \"\\n\";\n  await writeTextAtomic(\n    path,\n    `${text}${separator}${blank}${starterSection()}`,\n  );\n  return 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package/dist/{cli-6PGVHP7Y.js → cli-LUCSGTVI.js}

@@ -3,26 +3,26 @@ import {
   runAdd,
   runRemove,
   runUpdate
-} from "./chunk-7ZUCEMCY.js";
+} from "./chunk-IY7NYNPZ.js";
 import {
   runCheck
-} from "./chunk-JQU7FHYH.js";
+} from "./chunk-QW77LCOU.js";
 import {
   findingMessage,
   renderCheckGithub
-} from "./chunk-XWFNO5PO.js";
+} from "./chunk-GAJIJKET.js";
 import {
   renderCheckPretty,
   renderRemovePretty,
   renderUpdatePretty
-} from "./chunk-NGK3N6F2.js";
+} from "./chunk-T6SYGLWR.js";
 import {
   errorSite,
   shortCommit,
   shortLine,
   shortPin,
   shortSrc
-} from "./chunk-TA42STP7.js";
+} from "./chunk-UAKNZVCD.js";
 import {
   renderCheckJson,
   renderRemoveJson,
@@ -35,25 +35,21 @@ import {
   asCiteError,
   isCiteRule,
   spellSource
-} from "./chunk-UK2I3ACY.js";
+} from "./chunk-MHM4QEBV.js";
 import "./chunk-IKEWBMCN.js";
-import "./chunk-TU2WUBVZ.js";
-import "./chunk-TVIX653Q.js";
+import "./chunk-TLXE7LYK.js";
 import {
   terminalConfirm
-} from "./chunk-QCBICNKC.js";
-import "./chunk-3YHAYXBC.js";
+} from "./chunk-GREQKO6M.js";
 import {
   collect,
   configOption,
   explicitFalse,
   readStdin,
   reportConfig,
-  splitList
-} from "./chunk-NAZRLJAK.js";
-import {
+  splitList,
   splitPageArgument
-} from "./chunk-HVFR66GQ.js";
+} from "./chunk-TUAAR3MM.js";
 import {
   COMMON_FORMAT_LIST,
   OMITTED_WHEN_CLEAN,
@@ -63,10 +59,10 @@ import {
   isReportFormat,
   renderJunit,
   renderSarif
-} from "./chunk-TCC737IS.js";
+} from "./chunk-5G53XATW.js";
 import {
   STDIN_TOKEN
-} from "./chunk-527HHQPS.js";
+} from "./chunk-KCOFEWV5.js";
 import {
   fail
 } from "./chunk-YEUYKR62.js";
@@ -74,12 +70,14 @@ import {
   shouldColor
 } from "./chunk-RNVYGWIC.js";
 import "./chunk-MNH7QO4Z.js";
+import "./chunk-XKBEHKWO.js";
 import {
   notice
-} from "./chunk-Q35YIDBV.js";
+} from "./chunk-HX44GB4Z.js";
+import "./chunk-QCHVR4ZM.js";
 import {
   package_default
-} from "./chunk-6XTQDFGP.js";
+} from "./chunk-PCFG7E6B.js";
 import "./chunk-OWBRDNRZ.js";
 import "./chunk-G3T47CFV.js";
 import "./chunk-2H7UOFLK.js";
@@ -549,4 +547,4 @@ export {
   colorFor,
   splitPageArgument2 as splitPageArgument
 };
-//# sourceMappingURL=cli-6PGVHP7Y.js.map
+//# sourceMappingURL=cli-LUCSGTVI.js.map

package/dist/{cli-6PGVHP7Y.js.map → cli-LUCSGTVI.js.map}

@@ -1 +1 @@
-{"version":3,"sources":["../src/cite/cli.ts","../src/cite/reporters/sarif.ts","../src/cite/reporters/junit.ts"],"sourcesContent":["/**\n * The `cite` domain's commander program. Mounted by `src/cli.ts` under\n * `manni cite`; no entry point of its own. Grammar per proposal 0034: verbs are\n * `check`, `add`, `update`, `remove`; there is no default subcommand.\n *\n * Follows clig.dev as meta's does: primary output to stdout, diagnostics to\n * stderr, colour only on a TTY and never under `NO_COLOR`/`--no-color`, exit\n * `0` clean, `1` an error-severity finding, `2` operational/usage.\n */\nimport { Command, Option } from \"commander\";\nimport pkg from \"../../package.json\" with { type: \"json\" };\nimport {\n  collect,\n  configOption,\n  explicitFalse,\n  readStdin,\n  reportConfig,\n  splitList,\n} from \"../shared/cli-options.js\";\nimport { shouldColor } from \"../shared/color.js\";\nimport { splitPageArgument as splitSharedPageArgument } from \"../shared/pin.js\";\nimport { terminalConfirm } from \"../shared/prompt.js\";\nimport { fail } from \"../shared/run.js\";\nimport { notice } from \"../shared/warn.js\";\nimport {\n  COMMON_FORMAT_LIST,\n  OMITTED_WHEN_CLEAN,\n  REPORT_FORMAT_LIST,\n  STDIN_TOKEN,\n  isMachineFormat,\n} from \"../meta/internal.js\";\nimport { REPORT_FORMATS, isReportFormat } from \"../meta/index.js\";\nimport { runAdd } from \"./commands/add.js\";\nimport { runCheck } from \"./commands/check.js\";\nimport { runRemove } from \"./commands/remove.js\";\nimport { runUpdate } from \"./commands/update.js\";\nimport { CiteError, asCiteError } from \"./errors.js\";\nimport { spellSource } from \"./core/range.js\";\nimport { shortCommit, shortLine, shortPin, shortSrc } from \"./core/spell.js\";\nimport { renderCheckGithub } from \"./reporters/github.js\";\nimport { renderCheckJson, renderRemoveJson, renderUpdateJson } from \"./reporters/json.js\";\nimport { renderCheckJunit } from \"./reporters/junit.js\";\nimport { renderCheckPretty, renderRemovePretty, renderUpdatePretty } from \"./reporters/pretty.js\";\nimport { renderCheckSarif } from \"./reporters/sarif.js\";\nimport type { AddResult, PageLines } from \"./types.js\";\n\nconst UPDATE_FORMATS = [\"pretty\", \"json\"] as const;\ntype UpdateFormat = (typeof UPDATE_FORMATS)[number];\n/** The same two `update` has: a removal is a write, and writes report alike. */\nconst REMOVE_FORMATS = UPDATE_FORMATS;\ntype RemoveFormat = UpdateFormat;\n\n/**\n * Whether `command`'s output gets colour: this domain's `--no-color` and\n * `NO_COLOR` turn it off, and otherwise only a TTY turns it on\n * (`shouldColor`). `isTTY` is passed uncoerced: Node leaves it undefined off\n * a terminal, never false, and `shouldColor` reads a missing one as \"not a\n * terminal\".\n */\nexport function colorFor(\n  command: Command,\n  isTTY: boolean | undefined,\n  env?: NodeJS.ProcessEnv,\n): boolean {\n  // commander maps --no-color to opts.color === false, on the command that\n  // declares it.\n  const noColor = colorOwner(command).opts().color === false;\n  return shouldColor({ noColor, isTTY, env });\n}\n\n/**\n * The nearest command, this one or an ancestor, that declares `--no-color`:\n * the `cite` program, wherever it is mounted. Not the root: under the\n * umbrella that is `manni`, which has no `--no-color` of its own.\n */\nfunction colorOwner(command: Command): Command {\n  for (let c: Command | null = command; c !== null; c = c.parent) {\n    if (c.options.some((o) => o.long === \"--no-color\")) return c;\n  }\n  return command;\n}\n\nfunction isUpdateFormat(value: string): value is UpdateFormat {\n  return (UPDATE_FORMATS as readonly string[]).includes(value);\n}\n\nfunction isRemoveFormat(value: string): value is RemoveFormat {\n  return (REMOVE_FORMATS as readonly string[]).includes(value);\n}\n\n/**\n * Commander hands an `.action()` callback an untyped bag of option values, so\n * each subcommand declares the shape it actually reads. The `--no-<thing>`\n * flags are `boolean` and never `undefined`: commander supplies `true` when\n * the flag is absent, which is its default and not a choice, so only the\n * explicit `false` travels to the core (`explicitFalse`).\n */\ninterface InputCliOptions {\n  /** `--collection <name>`, repeatable; commander's default value is `[]`. */\n  collection: string[];\n  /** `--ext <list>`; the command splits it. */\n  ext?: string;\n  /** `--exclude <glob>`, repeatable; commander's default value is `[]`. */\n  exclude: string[];\n  /** `--as <format>`: force an extractor. */\n  as?: string;\n  /**\n   * `-c, --config <path>` and `--no-config` share one commander attribute:\n   * `undefined` with neither flag, the path with `-c`, `false` with\n   * `--no-config`. Split by `configOption`.\n   */\n  config?: string | boolean;\n  allowEmpty?: boolean;\n  /** `--no-gitignore`. */\n  gitignore: boolean;\n  /** `--root <dir>`: where `src:` paths resolve from. */\n  root?: string;\n}\n\ninterface CheckCliOptions extends InputCliOptions {\n  /** `-f, --format <format>`. Always a string: the declaration has a default. */\n  format: string;\n  quiet?: boolean;\n  /**\n   * `--baseline [path]` / `--no-baseline`, the same three-state split as\n   * `config`: absent leaves the config in charge, a string names a file, `true`\n   * is a bare `--baseline` (the default path), `false` is `--no-baseline`.\n   */\n  baseline?: string | boolean;\n  /** `--write-baseline [path]`; `true` for the bare flag. */\n  writeBaseline?: string | boolean;\n  /** `--no-check-sources`. */\n  checkSources: boolean;\n  showDiff?: boolean;\n  reveal?: boolean;\n}\n\ninterface AddCliOptions {\n  id?: string;\n  marker?: boolean;\n  quote?: boolean;\n  /** `--encrypt`. */\n  encrypt?: boolean;\n  /** `--no-commit-sha`. */\n  commitSha: boolean;\n  dryRun?: boolean;\n  as?: string;\n  root?: string;\n  config?: string | boolean;\n}\n\ninterface RemoveCliOptions extends Omit<InputCliOptions, \"root\"> {\n  /** `--only <id>`, repeatable; commander's default value is `[]`. */\n  only: string[];\n  dryRun?: boolean;\n  format: string;\n}\n\ninterface UpdateCliOptions extends InputCliOptions {\n  /** `--no-check-sources`: declared so the refusal names the flag rather than commander rejecting it. */\n  checkSources: boolean;\n  accept?: boolean;\n  recommit?: boolean;\n  /** `--only <id>`, repeatable; commander's default value is `[]`. */\n  only: string[];\n  dryRun?: boolean;\n  format: string;\n}\n\n/**\n * Split `docs/limits.md:9` or `docs/limits.md:14-18` into the page and the\n * claim's lines, under cite's error contract. The parsing is the shared pin\n * engine's (`splitPageArgument` in `src/shared/pin.ts`).\n */\nexport function splitPageArgument(arg: string): { page: string; lines?: PageLines } {\n  return asCiteError(() => splitSharedPageArgument(arg));\n}\n\n/** `line 9`, or `lines 14-18` for a range. */\nfunction spellAt(lines: PageLines, noun = \"line\"): string {\n  return lines.start === lines.end\n    ? `${noun} ${String(lines.start)}`\n    : `${noun}s ${String(lines.start)}-${String(lines.end)}`;\n}\n\n/**\n * What `add` says on success. One sentence composed from the result: what was\n * added, where it went, and what each end is pinned to. Lines are the page's\n * own, after the write. The source is spelled as it was written to the page,\n * abbreviated when it is a ciphertext, and quoted with its first pinned line\n * where the result carries one.\n */\nexport function addMessage(result: AddResult): string {\n  const { citation, claimLines } = result;\n  const claim = citation.claim;\n  const name = citation.id ?? (claim === undefined ? \"a bare pin\" : \"an entry\");\n  const src = shortSrc(spellSource(citation.source));\n  const commit = citation.source[\"commit-sha\"];\n  const quoted = result.sourceLine === undefined ? \"\" : shortLine(result.sourceLine);\n  const line = quoted === \"\" ? \"\" : ` \"${quoted}\"`;\n  const pin = `${src}${line}, ${shortPin(citation.source.integrity)}, ${commit === undefined ? \"no commit\" : shortCommit(commit)}`;\n  // Where it went: the page's own frontmatter, or the manifest that owns the\n  // page's citations, at the line the entry now sits on.\n  const where =\n    result.manifest === undefined\n      ? \"frontmatter\"\n      : `${result.manifest.file}:${String(result.manifest.line)}`;\n  const head = `${result.file}: added ${name} to ${where}`;\n\n  if (result.markerLine !== undefined) {\n    const at =\n      claimLines === undefined ? \"\" : `, claim pinned at ${spellAt(claimLines)}`;\n    const wrote = result.markerJoined === true ? \"joined the marker at line\" : \"marker at line\";\n    const marked = `${head}; ${wrote} ${String(result.markerLine)}${at}`;\n    if (claim === undefined) return marked;\n    if (citation.quote === true) return `${marked} (a block that reproduces ${src})`;\n    return `${marked} (${shortPin(claim.integrity)}; source ${pin})`;\n  }\n  if (claim === undefined || claimLines === undefined) {\n    return `${head} (source ${pin})`;\n  }\n  if (citation.quote === true) {\n    return `${head} (claim ${spellAt(claimLines, \"line\")}, a block that reproduces ${src})`;\n  }\n  return `${head} (claim at ${spellAt(claimLines)}, ${shortPin(claim.integrity)}; source ${pin})`;\n}\n\nexport function buildProgram(): Command {\n  const program = new Command();\n  program\n    .name(\"cite\")\n    .description(\n      \"Track citations from doc claims to source lines and check them for drift.\",\n    )\n    .version(pkg.version, \"-V, --version\")\n    .option(\"--no-color\", \"disable colored output\")\n    // A pointer, not the whole help screen: the message that precedes it\n    // already names the offending flag.\n    .showHelpAfterError(\"(add --help for usage)\")\n    // MUST come before the `.command()` calls below. `copyInheritedSettings`\n    // copies `_exitCallback` by value at subcommand-creation time, so an\n    // `exitOverride()` installed afterwards leaves every subcommand still\n    // calling `process.exit(1)`.\n    .exitOverride();\n\n  program\n    .command(\"check\")\n    .description(\"Check every citation in the given pages against its source\")\n    .argument(\n      \"[paths...]\",\n      \"files, directories, or globs to check (use - for stdin)\",\n    )\n    .option(\n      \"--collection <name>\",\n      \"configured collection to run over; repeatable\",\n      collect,\n      [],\n    )\n    .option(\"--ext <list>\", \"comma-separated extensions for directory walks\")\n    .option(\"--exclude <glob>\", \"glob to exclude; repeatable\", collect, [])\n    .option(\"--as <format>\", \"force an input format for every input\")\n    .option(\n      \"-f, --format <format>\",\n      `output: ${REPORT_FORMATS.join(\" | \")}`,\n      \"pretty\",\n    )\n    .option(\"-c, --config <path>\", \"path to a manni config file\")\n    .option(\"--no-config\", \"ignore any discovered config file\")\n    .option(\"-q, --quiet\", \"in pretty output, hide current citations and clean files\")\n    .option(\"--allow-empty\", \"treat zero matched files as success\")\n    .option(\"--no-gitignore\", \"check files .gitignore covers\")\n    // No `defaultValue` and no `.preset()`, for the reasons meta's validate\n    // gives: a bare flag must stay distinguishable from a typed path.\n    .addOption(\n      new Option(\n        \"--baseline [path]\",\n        \"compare against a baseline; fail only on findings not in it\",\n      ),\n    )\n    .addOption(\n      new Option(\n        \"--write-baseline [path]\",\n        \"record current findings as the baseline, then exit 0\",\n      ),\n    )\n    .option(\"--no-baseline\", \"ignore a baseline configured by `baseline:`\")\n    .option(\"--no-check-sources\", \"page-side rules only; every source status is skipped\")\n    .option(\n      \"--root <dir>\",\n      \"directory src: paths resolve from (default: cite.root from config, else the git root, else the current directory)\",\n    )\n    .option(\"--show-diff\", \"in pretty output, print the diff and commit subjects for changed\")\n    .option(\"--reveal\", \"in pretty output, print the decrypted path beside an encrypted source\")\n    .addHelpText(\n      \"after\",\n      [\n        \"\",\n        \"Examples:\",\n        \"  manni cite check docs/                          # walk a directory\",\n        \"  manni cite check --collection guides             # one configured collection\",\n        '  manni cite check \"docs/**/*.md\" -f github        # CI annotations',\n        \"  manni cite check --show-diff docs/limits.md      # see what changed\",\n        \"  manni cite check --baseline                      # fail only on new findings\",\n        \"  cat page.md | manni cite check - --as markdown\",\n      ].join(\"\\n\"),\n    )\n    .action(async (paths: string[], options: CheckCliOptions, command: Command) => {\n      try {\n        const format = options.format;\n        if (!isReportFormat(format)) {\n          throw new CiteError(\n            `Unknown --format \"${format}\". Use ${REPORT_FORMAT_LIST}.`,\n          );\n        }\n        const exts = options.ext ? splitList(options.ext) : undefined;\n        const stdinContent = paths.includes(STDIN_TOKEN) ? await readStdin() : undefined;\n        const cwd = process.cwd();\n\n        const run = await runCheck({\n          inputs: paths,\n          collection: options.collection,\n          exts,\n          exclude: options.exclude,\n          as: options.as,\n          ...configOption(options.config),\n          onConfigLoaded: reportConfig(!isMachineFormat(format), cwd),\n          stdinContent,\n          // `undefined` rather than `false` when absent, so config still wins.\n          allowEmpty: options.allowEmpty ? true : undefined,\n          respectGitignore: explicitFalse(options.gitignore),\n          onNotice: notice,\n          baseline: options.baseline,\n          writeBaseline: options.writeBaseline,\n          checkSources: explicitFalse(options.checkSources),\n          // Only so the run can say git is not there to give diffs; the diffs\n          // themselves are the pretty reporter's.\n          showDiff: options.showDiff ? true : undefined,\n          root: options.root,\n        });\n\n        let text: string;\n        switch (format) {\n          case \"pretty\":\n            text = renderCheckPretty(run, {\n              color: colorFor(command, process.stdout.isTTY),\n              quiet: Boolean(options.quiet),\n              showDiff: Boolean(options.showDiff),\n              reveal: Boolean(options.reveal),\n            });\n            break;\n          case \"json\":\n            text = renderCheckJson(run);\n            break;\n          case \"github\":\n            text = renderCheckGithub(run);\n            break;\n          case \"sarif\":\n            text = renderCheckSarif(run, { onNotice: notice });\n            break;\n          case \"junit\":\n            text = renderCheckJunit(run);\n            break;\n        }\n        // Only `github` may say nothing on a clean run; every other format\n        // owes its envelope even when empty.\n        if (text.length > 0 || !OMITTED_WHEN_CLEAN.has(format)) {\n          process.stdout.write(`${text}\\n`);\n        }\n        // `failed` counts files with an unbaselined error-severity finding;\n        // warnings never move it.\n        process.exitCode = run.summary.failed > 0 ? 1 : 0;\n      } catch (err) {\n        fail(err);\n      }\n    });\n\n  program\n    .command(\"add\")\n    .description(\"Mint a citation for a source range and write it to a page\")\n    .argument(\n      \"<page>\",\n      \"the page to cite from, with the claim's lines: page:L or page:L1-L2 (use - for stdin, with --as)\",\n    )\n    .argument(\n      \"<src>\",\n      \"path, path:L or path:L1-L2 relative to --root, or an encrypted ~source with the same line forms\",\n    )\n    .option(\"--id <id>\", \"kebab-case id, unique on the page; required with --marker\")\n    .option(\"--marker\", \"write a cite <id> marker above the paragraph holding the page lines and pin the text it anchors\")\n    .option(\"--quote\", \"the page lines are a fenced block that reproduces the source\")\n    .option(\n      \"--encrypt\",\n      \"write source.file encrypted, with an hmac-sha256- pin; with no key, offer to create one (an available key encrypts without the flag)\",\n    )\n    .option(\"--no-commit-sha\", \"do not record HEAD\")\n    .option(\"--dry-run\", \"print the diff; write nothing\")\n    .option(\"--as <format>\", \"force the page format\")\n    .option(\"--root <dir>\", \"directory source paths resolve from (as check)\")\n    .option(\"-c, --config <path>\", \"path to a manni config file\")\n    .option(\"--no-config\", \"ignore any discovered config file\")\n    .addHelpText(\n      \"after\",\n      [\n        \"\",\n        \"Examples:\",\n        \"  manni cite add docs/limits.md:9 lib/limits.ts:2 --id fetch-timeout\",\n        \"  manni cite add docs/limits.md:30 lib/limits.ts:8-12 --id timeouts --marker\",\n        \"  manni cite add docs/limits.md:14-18 lib/limits.ts:1-3 --quote\",\n        \"  manni cite add docs/limits.md lib/limits.ts --dry-run\",\n        \"  cat page.md | manni cite add -:9 lib/limits.ts:2 --as markdown > out.md\",\n      ].join(\"\\n\"),\n    )\n    .action(async (pageArgument: string, src: string, options: AddCliOptions) => {\n      try {\n        const { page, lines } = splitPageArgument(pageArgument);\n        const usingStdin = page === STDIN_TOKEN;\n        const stdinContent = usingStdin ? await readStdin() : undefined;\n        const dryRun = Boolean(options.dryRun);\n        const cwd = process.cwd();\n\n        const result = await runAdd({\n          page,\n          pageLines: lines,\n          src,\n          id: options.id,\n          marker: options.marker ? true : undefined,\n          quote: options.quote ? true : undefined,\n          // `undefined` when absent, so the key decides: an available one\n          // encrypts without the flag.\n          encrypt: options.encrypt ? true : undefined,\n          commitSha: explicitFalse(options.commitSha),\n          dryRun,\n          as: options.as,\n          ...configOption(options.config),\n          // With `-` the page owns stdout; so does the diff under --dry-run.\n          onConfigLoaded: reportConfig(!usingStdin && !dryRun, cwd),\n          stdinContent,\n          root: options.root,\n          onNotice: notice,\n          // Only on a terminal: off one, a missing key is a refusal, not a\n          // question nobody can answer. With `-` stdin is the page, so no\n          // question is put either.\n          confirm: terminalConfirm(),\n        });\n\n        const message = addMessage(result);\n        // A dry run prints every diff the write would make: the page's, and\n        // the manifest's when the entry goes there.\n        const diffs = [result.diff, result.manifest?.diff ?? \"\"].filter((d) => d.length > 0);\n        if (usingStdin) {\n          // The rewritten page owns stdout; everything else is a diagnostic.\n          process.stdout.write(result.content);\n          if (dryRun) for (const diff of diffs) process.stderr.write(`${diff}\\n`);\n          process.stderr.write(`${message}\\n`);\n        } else if (dryRun) {\n          for (const diff of diffs) process.stdout.write(`${diff}\\n`);\n          process.stderr.write(`${message}\\n`);\n        } else {\n          process.stdout.write(`${message}\\n`);\n        }\n        process.exitCode = 0;\n      } catch (err) {\n        fail(err);\n      }\n    });\n\n  program\n    .command(\"update\")\n    .description(\"Rewrite moved citations in place; with --accept, re-mint changed ones\")\n    .argument(\n      \"[paths...]\",\n      \"files, directories, or globs to update (use - for stdin)\",\n    )\n    .option(\n      \"--collection <name>\",\n      \"configured collection to run over; repeatable\",\n      collect,\n      [],\n    )\n    .option(\"--ext <list>\", \"comma-separated extensions for directory walks\")\n    .option(\"--exclude <glob>\", \"glob to exclude; repeatable\", collect, [])\n    .option(\"--as <format>\", \"force an input format for every input\")\n    .option(\"-c, --config <path>\", \"path to a manni config file\")\n    .option(\"--no-config\", \"ignore any discovered config file\")\n    .option(\"--allow-empty\", \"treat zero matched files as success\")\n    .option(\"--no-gitignore\", \"update files .gitignore covers\")\n    .option(\"--no-check-sources\", \"refused: update needs the sources\")\n    .option(\"--root <dir>\", \"directory src: paths resolve from (as check)\")\n    .option(\"--accept\", \"re-mint changed and never-true entries at HEAD; prints old and new pins\")\n    .option(\n      \"--recommit\",\n      \"re-record commit-sha where the recorded commit does not contain the pinned lines, or is outside HEAD's history\",\n    )\n    .option(\"--only <id>\", \"limit to entries with this id; repeatable\", collect, [])\n    .option(\"--dry-run\", \"print the diffs; write nothing\")\n    .option(\n      \"-f, --format <format>\",\n      `output: ${UPDATE_FORMATS.join(\" | \")}`,\n      \"pretty\",\n    )\n    .addHelpText(\n      \"after\",\n      [\n        \"\",\n        \"Examples:\",\n        \"  manni cite update docs/                          # rewrite moved entries\",\n        \"  manni cite update --accept --only fetch-timeout docs/limits.md\",\n        \"  manni cite update --dry-run docs/               # see the diffs first\",\n        \"  manni cite update --recommit docs/               # repair unsupported commit-sha\",\n      ].join(\"\\n\"),\n    )\n    .action(async (paths: string[], options: UpdateCliOptions, command: Command) => {\n      try {\n        const format = options.format;\n        if (!isUpdateFormat(format)) {\n          throw new CiteError(\n            `Unknown --format \"${format}\". Use ${COMMON_FORMAT_LIST}.`,\n          );\n        }\n        if (!options.checkSources) {\n          throw new CiteError(\n            \"update needs the sources: drop --no-check-sources (or `checkSources: false`).\",\n          );\n        }\n        const exts = options.ext ? splitList(options.ext) : undefined;\n        const usingStdin = paths.includes(STDIN_TOKEN);\n        const stdinContent = usingStdin ? await readStdin() : undefined;\n        const dryRun = Boolean(options.dryRun);\n        // With `-` the rewritten page owns stdout, as it does for `add -`; a\n        // dry run prints the diffs instead, so the report keeps stdout.\n        const pageToStdout = usingStdin && !dryRun;\n        const cwd = process.cwd();\n\n        const run = await runUpdate({\n          inputs: paths,\n          collection: options.collection,\n          exts,\n          exclude: options.exclude,\n          as: options.as,\n          ...configOption(options.config),\n          onConfigLoaded: reportConfig(format === \"pretty\" && !pageToStdout, cwd),\n          stdinContent,\n          allowEmpty: options.allowEmpty ? true : undefined,\n          respectGitignore: explicitFalse(options.gitignore),\n          onNotice: notice,\n          root: options.root,\n          accept: options.accept ? true : undefined,\n          recommit: options.recommit ? true : undefined,\n          only: options.only.length > 0 ? options.only : undefined,\n          dryRun,\n        });\n\n        const text =\n          format === \"json\"\n            ? renderUpdateJson(run)\n            : renderUpdatePretty(run, {\n                color: colorFor(command, process.stdout.isTTY),\n                // The diffs are the point of a dry run; a real run prints\n                // what it rewrote and leaves the file to say the rest.\n                showDiff: dryRun,\n              });\n        const stdinPage = pageToStdout ? run.pages.find((page) => page.content !== undefined) : undefined;\n        if (stdinPage?.content !== undefined) {\n          process.stdout.write(stdinPage.content);\n          process.stderr.write(`${text}\\n`);\n        } else {\n          process.stdout.write(`${text}\\n`);\n        }\n        // Exit 1 when something was skipped with an error-severity finding:\n        // work left undone, `fill`'s precedent.\n        process.exitCode = run.exitCode;\n      } catch (err) {\n        fail(err);\n      }\n    });\n\n  program\n    .command(\"remove\")\n    .description(\"Remove the named citations from the given pages, markers and all\")\n    .argument(\n      \"[paths...]\",\n      \"files, directories, or globs to remove from (use - for stdin)\",\n    )\n    .option(\n      \"--collection <name>\",\n      \"configured collection to run over; repeatable\",\n      collect,\n      [],\n    )\n    .option(\"--ext <list>\", \"comma-separated extensions for directory walks\")\n    .option(\"--exclude <glob>\", \"glob to exclude; repeatable\", collect, [])\n    .option(\"--as <format>\", \"force an input format for every input\")\n    .option(\"-c, --config <path>\", \"path to a manni config file\")\n    .option(\"--no-config\", \"ignore any discovered config file\")\n    .option(\"--allow-empty\", \"treat zero matched files as success\")\n    .option(\"--no-gitignore\", \"remove from files .gitignore covers\")\n    .option(\n      \"--only <id>\",\n      \"the entry to remove, by id or by pointer (/citations/N); required, and repeatable\",\n      collect,\n      [],\n    )\n    .option(\"--dry-run\", \"print the diffs and the report; write nothing\")\n    .option(\n      \"-f, --format <format>\",\n      `output: ${REMOVE_FORMATS.join(\" | \")}`,\n      \"pretty\",\n    )\n    .addHelpText(\n      \"after\",\n      [\n        \"\",\n        \"Examples:\",\n        \"  manni cite remove docs/limits.md --only fetch-timeout\",\n        \"  manni cite remove docs/ --only fetch-timeout --only retries --dry-run\",\n        \"  manni cite remove --collection site --only /citations/3 -f json\",\n      ].join(\"\\n\"),\n    )\n    .action(async (paths: string[], options: RemoveCliOptions, command: Command) => {\n      try {\n        const format = options.format;\n        if (!isRemoveFormat(format)) {\n          throw new CiteError(\n            `Unknown --format \"${format}\". Use ${COMMON_FORMAT_LIST}.`,\n          );\n        }\n        const exts = options.ext ? splitList(options.ext) : undefined;\n        const usingStdin = paths.includes(STDIN_TOKEN);\n        const stdinContent = usingStdin ? await readStdin() : undefined;\n        const dryRun = Boolean(options.dryRun);\n        // With `-` the rewritten page owns stdout, exactly as on `update -`.\n        const pageToStdout = usingStdin && !dryRun;\n        const cwd = process.cwd();\n\n        const run = await runRemove({\n          inputs: paths,\n          collection: options.collection,\n          exts,\n          exclude: options.exclude,\n          as: options.as,\n          ...configOption(options.config),\n          onConfigLoaded: reportConfig(format === \"pretty\" && !pageToStdout, cwd),\n          stdinContent,\n          allowEmpty: options.allowEmpty ? true : undefined,\n          respectGitignore: explicitFalse(options.gitignore),\n          onNotice: notice,\n          only: options.only,\n          dryRun,\n        });\n\n        const text =\n          format === \"json\"\n            ? renderRemoveJson(run)\n            : renderRemovePretty(run, {\n                color: colorFor(command, process.stdout.isTTY),\n                // The diffs are the point of a dry run; a real run prints\n                // what it removed and leaves the file to say the rest.\n                showDiff: dryRun,\n                dryRun,\n              });\n        const stdinPage = pageToStdout ? run.pages.find((page) => page.content !== undefined) : undefined;\n        if (stdinPage?.content !== undefined) {\n          process.stdout.write(stdinPage.content);\n          process.stderr.write(`${text}\\n`);\n        } else {\n          process.stdout.write(`${text}\\n`);\n        }\n        // Everything named was removed, or previewed: there is no exit 1.\n        process.exitCode = 0;\n      } catch (err) {\n        fail(err);\n      }\n    });\n\n  return program;\n}\n","/**\n * SARIF for `check`. Meta's renderer builds the envelope, the\n * repository-relative uris and the fingerprints the baseline shares, from the\n * adapted results. What it cannot know is what a cite rule is: it describes\n * every rule as a schema keyword, links meta's fix page, and prefixes each\n * message with the JSON Pointer of the entry, `(root)` for a finding about no\n * entry. This renderer replaces those three with the cite rule's own\n * description, a link to its row of the citations reference, and the message\n * the github annotation carries, which names the citation the pointer only\n * numbered. A message is no part of a fingerprint, so the baseline is\n * unaffected.\n */\nimport { renderSarif, type ValidationResult } from \"../../meta/index.js\";\nimport { errorSite } from \"../core/adapt.js\";\nimport { RULE_ID_PREFIX, isCiteRule } from \"../core/severity.js\";\nimport type { CheckRun, CiteRule } from \"../types.js\";\nimport { findingMessage } from \"./github.js\";\n\nconst INFORMATION_URI = \"https://hawkeyexl.github.io/manni/cite/\";\n\n/** The citations reference, whose rule tables anchor each row by rule name. */\nconst RULES_URI = \"https://hawkeyexl.github.io/manni/cite/reference/citations/\";\n\n/** What each rule is, as the citations reference's tables say it. */\nconst RULE_DESCRIPTIONS: Readonly<Record<CiteRule, string>> = {\n  \"source-moved\": \"The cited source lines moved to one other place in the file.\",\n  \"source-moved-ambiguous\": \"The cited source lines now match at several places in the file.\",\n  \"source-changed\": \"The cited source lines changed since the citation pinned them.\",\n  \"source-never-true\": \"The pin never matched the source at the recorded commit.\",\n  \"source-missing\": \"The cited source file is not tracked under the root, or cannot be decrypted.\",\n  \"claim-moved\": \"The cited sentence moved to other lines of the page.\",\n  \"claim-moved-ambiguous\": \"The cited sentence now appears at several places on the page.\",\n  \"claim-reanchored\": \"The cited sentence's words are unchanged since the claim's baseline, and only its layout moved.\",\n  \"claim-changed\": \"The cited sentence was edited since the citation pinned it.\",\n  \"marker-orphan\": \"A marker names an id no citation has.\",\n  \"marker-invalid\": \"A marker is malformed, or the page has too many markers.\",\n  \"marker-repeated\": \"Two markers name the same citation id.\",\n  \"marker-misplaced\": \"A marker line sits inside the paragraph it anchors, and splits it.\",\n  \"anchor-invalid\": \"A citation's anchor cannot work.\",\n  \"entry-invalid\": \"A citation entry is malformed.\",\n  \"quote-drift\": \"A quoted block no longer reproduces its source.\",\n};\n\n/**\n * The label meta's reporters put before a message: `(root) ` for a finding\n * about no entry, `/citations/N ` for one about an entry. Nothing else ever\n * opens a cite finding's adapted message.\n */\nexport const ENTRY_LABEL = /^(?:\\(root\\)|\\/citations\\/\\d+) /;\n\nexport interface SarifRule {\n  id: string;\n  shortDescription: { text: string };\n  helpUri?: string;\n}\n\n/** As much of meta's SARIF as this renderer and its tests read back. */\nexport interface SarifLog {\n  runs: {\n    tool: { driver: { informationUri: string; rules: SarifRule[] } };\n    results: { ruleId: string; message: { text: string } }[];\n  }[];\n}\n\n/**\n * The adapted results with each message rewritten as the github annotation\n * says it. An error is paired with its finding by rule, entry, line and\n * message, as the baseline split pairs them; the baseline has already\n * dropped the errors it forgives.\n */\nexport function withFindingMessages(run: CheckRun): ValidationResult[] {\n  return run.results.map((result) => {\n    const page = run.pages.find((p) => p.file === result.file);\n    if (page === undefined) return result;\n    const errors = result.errors.map((error) => {\n      const finding = page.findings.find(\n        (f) =>\n          f.rule === error.keyword &&\n          (f.index === undefined ? \"\" : `/citations/${String(f.index)}`) === error.instancePath &&\n          f.message === error.message &&\n          (errorSite(f).line ?? null) === (error.line ?? null),\n      );\n      return finding === undefined ? error : { ...error, message: findingMessage(finding) };\n    });\n    return { ...result, errors };\n  });\n}\n\n/** A rule as the citation tool describes it. */\nfunction describe(rule: SarifRule): SarifRule {\n  const name = rule.id.slice(RULE_ID_PREFIX.length + 1);\n  if (!isCiteRule(name)) return rule;\n  return { id: rule.id, shortDescription: { text: RULE_DESCRIPTIONS[name] }, helpUri: `${RULES_URI}#${name}` };\n}\n\nexport function renderCheckSarif(run: CheckRun, opts: { onNotice?: (message: string) => void } = {}): string {\n  const log = JSON.parse(\n    renderSarif(withFindingMessages(run), {\n      frame: run.frame,\n      ...(opts.onNotice === undefined ? {} : { onNotice: opts.onNotice }),\n    }),\n  ) as SarifLog;\n  for (const sarifRun of log.runs) {\n    sarifRun.tool.driver.informationUri = INFORMATION_URI;\n    sarifRun.tool.driver.rules = sarifRun.tool.driver.rules.map(describe);\n    for (const result of sarifRun.results) result.message.text = result.message.text.replace(ENTRY_LABEL, \"\");\n  }\n  return JSON.stringify(log, null, 2);\n}\n","/**\n * JUnit for `check`: meta's renderer over the adapted results, under the\n * `manni.cite` classname, with each failure's message the one the github\n * annotation carries.\n * Meta's renderer opens every message with the entry's JSON Pointer, `(root)`\n * for a finding about no entry, which says nothing about a citation. The\n * failure's `type` is already the rule id.\n */\nimport { renderJunit } from \"../../meta/index.js\";\nimport type { CheckRun } from \"../types.js\";\nimport { ENTRY_LABEL, withFindingMessages } from \"./sarif.js\";\n\n/** JUnit `classname` for the citation tool's findings. */\nexport const JUNIT_CLASSNAME = \"manni.cite\";\n\n/** A `message=\"` attribute's opening label. The value is escaped, so `message=\"` opens nothing else. */\nconst MESSAGE_LABEL = new RegExp(`message=\"${ENTRY_LABEL.source.replace(/^\\^/, \"\")}`, \"g\");\n\nexport function renderCheckJunit(run: CheckRun): string {\n  return renderJunit(withFindingMessages(run), { frame: run.frame, classname: JUNIT_CLASSNAME }).replace(\n    MESSAGE_LABEL,\n    'message=\"',\n  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${wrote} ${String(result.markerLine)}${at}`;\n    if (claim === undefined) return marked;\n    if (citation.quote === true) return `${marked} (a block that reproduces ${src})`;\n    return `${marked} (${shortPin(claim.integrity)}; source ${pin})`;\n  }\n  if (claim === undefined || claimLines === undefined) {\n    return `${head} (source ${pin})`;\n  }\n  if (citation.quote === true) {\n    return `${head} (claim ${spellAt(claimLines, \"line\")}, a block that reproduces ${src})`;\n  }\n  return `${head} (claim at ${spellAt(claimLines)}, ${shortPin(claim.integrity)}; source ${pin})`;\n}\n\nexport function buildProgram(): Command {\n  const program = new Command();\n  program\n    .name(\"cite\")\n    .description(\n      \"Track citations from doc claims to source lines and check them for drift.\",\n    )\n    .version(pkg.version, \"-V, --version\")\n    .option(\"--no-color\", \"disable colored output\")\n    // A pointer, not the whole help screen: the message that precedes it\n    // already names the offending flag.\n    .showHelpAfterError(\"(add --help for usage)\")\n    // MUST come before the `.command()` calls below. `copyInheritedSettings`\n    // copies `_exitCallback` by value at subcommand-creation time, so an\n    // `exitOverride()` installed afterwards leaves every subcommand still\n    // calling `process.exit(1)`.\n    .exitOverride();\n\n  program\n    .command(\"check\")\n    .description(\"Check every citation in the given pages against its source\")\n    .argument(\n      \"[paths...]\",\n      \"files, directories, or globs to check (use - for stdin)\",\n    )\n    .option(\n      \"--collection <name>\",\n      \"configured collection to run over; repeatable\",\n      collect,\n      [],\n    )\n    .option(\"--ext <list>\", \"comma-separated extensions for directory walks\")\n    .option(\"--exclude <glob>\", \"glob to exclude; repeatable\", collect, [])\n    .option(\"--as <format>\", \"force an input format for every input\")\n    .option(\n      \"-f, --format <format>\",\n      `output: ${REPORT_FORMATS.join(\" | \")}`,\n      \"pretty\",\n    )\n    .option(\"-c, --config <path>\", \"path to a manni config file\")\n    .option(\"--no-config\", \"ignore any discovered config file\")\n    .option(\"-q, --quiet\", \"in pretty output, hide current citations and clean files\")\n    .option(\"--allow-empty\", \"treat zero matched files as success\")\n    .option(\"--no-gitignore\", \"check files .gitignore covers\")\n    // No `defaultValue` and no `.preset()`, for the reasons meta's validate\n    // gives: a bare flag must stay distinguishable from a typed path.\n    .addOption(\n      new Option(\n        \"--baseline [path]\",\n        \"compare against a baseline; fail only on findings not in it\",\n      ),\n    )\n    .addOption(\n      new Option(\n        \"--write-baseline [path]\",\n        \"record current findings as the baseline, then exit 0\",\n      ),\n    )\n    .option(\"--no-baseline\", \"ignore a baseline configured by `baseline:`\")\n    .option(\"--no-check-sources\", \"page-side rules only; every source status is skipped\")\n    .option(\n      \"--root <dir>\",\n      \"directory src: paths resolve from (default: cite.root from config, else the git root, else the current directory)\",\n    )\n    .option(\"--show-diff\", \"in pretty output, print the diff and commit subjects for changed\")\n    .option(\"--reveal\", \"in pretty output, print the decrypted path beside an encrypted source\")\n    .addHelpText(\n      \"after\",\n      [\n        \"\",\n        \"Examples:\",\n        \"  manni cite check docs/                          # walk a directory\",\n        \"  manni cite check --collection guides             # one configured collection\",\n        '  manni cite check \"docs/**/*.md\" -f github        # CI annotations',\n        \"  manni cite check --show-diff docs/limits.md      # see what changed\",\n        \"  manni cite check --baseline                      # fail only on new findings\",\n        \"  cat page.md | manni cite check - --as markdown\",\n      ].join(\"\\n\"),\n    )\n    .action(async (paths: string[], options: CheckCliOptions, command: Command) => {\n      try {\n        const format = options.format;\n        if (!isReportFormat(format)) {\n          throw new CiteError(\n            `Unknown --format \"${format}\". Use ${REPORT_FORMAT_LIST}.`,\n          );\n        }\n        const exts = options.ext ? splitList(options.ext) : undefined;\n        const stdinContent = paths.includes(STDIN_TOKEN) ? await readStdin() : undefined;\n        const cwd = process.cwd();\n\n        const run = await runCheck({\n          inputs: paths,\n          collection: options.collection,\n          exts,\n          exclude: options.exclude,\n          as: options.as,\n          ...configOption(options.config),\n          onConfigLoaded: reportConfig(!isMachineFormat(format), cwd),\n          stdinContent,\n          // `undefined` rather than `false` when absent, so config still wins.\n          allowEmpty: options.allowEmpty ? true : undefined,\n          respectGitignore: explicitFalse(options.gitignore),\n          onNotice: notice,\n          baseline: options.baseline,\n          writeBaseline: options.writeBaseline,\n          checkSources: explicitFalse(options.checkSources),\n          // Only so the run can say git is not there to give diffs; the diffs\n          // themselves are the pretty reporter's.\n          showDiff: options.showDiff ? true : undefined,\n          root: options.root,\n        });\n\n        let text: string;\n        switch (format) {\n          case \"pretty\":\n            text = renderCheckPretty(run, {\n              color: colorFor(command, process.stdout.isTTY),\n              quiet: Boolean(options.quiet),\n              showDiff: Boolean(options.showDiff),\n              reveal: Boolean(options.reveal),\n            });\n            break;\n          case \"json\":\n            text = renderCheckJson(run);\n            break;\n          case \"github\":\n            text = renderCheckGithub(run);\n            break;\n          case \"sarif\":\n            text = renderCheckSarif(run, { onNotice: notice });\n            break;\n          case \"junit\":\n            text = renderCheckJunit(run);\n            break;\n        }\n        // Only `github` may say nothing on a clean run; every other format\n        // owes its envelope even when empty.\n        if (text.length > 0 || !OMITTED_WHEN_CLEAN.has(format)) {\n          process.stdout.write(`${text}\\n`);\n        }\n        // `failed` counts files with an unbaselined error-severity finding;\n        // warnings never move it.\n        process.exitCode = run.summary.failed > 0 ? 1 : 0;\n      } catch (err) {\n        fail(err);\n      }\n    });\n\n  program\n    .command(\"add\")\n    .description(\"Mint a citation for a source range and write it to a page\")\n    .argument(\n      \"<page>\",\n      \"the page to cite from, with the claim's lines: page:L or page:L1-L2 (use - for stdin, with --as)\",\n    )\n    .argument(\n      \"<src>\",\n      \"path, path:L or path:L1-L2 relative to --root, or an encrypted ~source with the same line forms\",\n    )\n    .option(\"--id <id>\", \"kebab-case id, unique on the page; required with --marker\")\n    .option(\"--marker\", \"write a cite <id> marker above the paragraph holding the page lines and pin the text it anchors\")\n    .option(\"--quote\", \"the page lines are a fenced block that reproduces the source\")\n    .option(\n      \"--encrypt\",\n      \"write source.file encrypted, with an hmac-sha256- pin; with no key, offer to create one (an available key encrypts without the flag)\",\n    )\n    .option(\"--no-commit-sha\", \"do not record HEAD\")\n    .option(\"--dry-run\", \"print the diff; write nothing\")\n    .option(\"--as <format>\", \"force the page format\")\n    .option(\"--root <dir>\", \"directory source paths resolve from (as check)\")\n    .option(\"-c, --config <path>\", \"path to a manni config file\")\n    .option(\"--no-config\", \"ignore any discovered config file\")\n    .addHelpText(\n      \"after\",\n      [\n        \"\",\n        \"Examples:\",\n        \"  manni cite add docs/limits.md:9 lib/limits.ts:2 --id fetch-timeout\",\n        \"  manni cite add docs/limits.md:30 lib/limits.ts:8-12 --id timeouts --marker\",\n        \"  manni cite add docs/limits.md:14-18 lib/limits.ts:1-3 --quote\",\n        \"  manni cite add docs/limits.md lib/limits.ts --dry-run\",\n        \"  cat page.md | manni cite add -:9 lib/limits.ts:2 --as markdown > out.md\",\n      ].join(\"\\n\"),\n    )\n    .action(async (pageArgument: string, src: string, options: AddCliOptions) => {\n      try {\n        const { page, lines } = splitPageArgument(pageArgument);\n        const usingStdin = page === STDIN_TOKEN;\n        const stdinContent = usingStdin ? await readStdin() : undefined;\n        const dryRun = Boolean(options.dryRun);\n        const cwd = process.cwd();\n\n        const result = await runAdd({\n          page,\n          pageLines: lines,\n          src,\n          id: options.id,\n          marker: options.marker ? true : undefined,\n          quote: options.quote ? true : undefined,\n          // `undefined` when absent, so the key decides: an available one\n          // encrypts without the flag.\n          encrypt: options.encrypt ? true : undefined,\n          commitSha: explicitFalse(options.commitSha),\n          dryRun,\n          as: options.as,\n          ...configOption(options.config),\n          // With `-` the page owns stdout; so does the diff under --dry-run.\n          onConfigLoaded: reportConfig(!usingStdin && !dryRun, cwd),\n          stdinContent,\n          root: options.root,\n          onNotice: notice,\n          // Only on a terminal: off one, a missing key is a refusal, not a\n          // question nobody can answer. With `-` stdin is the page, so no\n          // question is put either.\n          confirm: terminalConfirm(),\n        });\n\n        const message = addMessage(result);\n        // A dry run prints every diff the write would make: the page's, and\n        // the manifest's when the entry goes there.\n        const diffs = [result.diff, result.manifest?.diff ?? \"\"].filter((d) => d.length > 0);\n        if (usingStdin) {\n          // The rewritten page owns stdout; everything else is a diagnostic.\n          process.stdout.write(result.content);\n          if (dryRun) for (const diff of diffs) process.stderr.write(`${diff}\\n`);\n          process.stderr.write(`${message}\\n`);\n        } else if (dryRun) {\n          for (const diff of diffs) process.stdout.write(`${diff}\\n`);\n          process.stderr.write(`${message}\\n`);\n        } else {\n          process.stdout.write(`${message}\\n`);\n        }\n        process.exitCode = 0;\n      } catch (err) {\n        fail(err);\n      }\n    });\n\n  program\n    .command(\"update\")\n    .description(\"Rewrite moved citations in place; with --accept, re-mint changed ones\")\n    .argument(\n      \"[paths...]\",\n      \"files, directories, or globs to update (use - for stdin)\",\n    )\n    .option(\n      \"--collection <name>\",\n      \"configured collection to run over; repeatable\",\n      collect,\n      [],\n    )\n    .option(\"--ext <list>\", \"comma-separated extensions for directory walks\")\n    .option(\"--exclude <glob>\", \"glob to exclude; repeatable\", collect, [])\n    .option(\"--as <format>\", \"force an input format for every input\")\n    .option(\"-c, --config <path>\", \"path to a manni config file\")\n    .option(\"--no-config\", \"ignore any discovered config file\")\n    .option(\"--allow-empty\", \"treat zero matched files as success\")\n    .option(\"--no-gitignore\", \"update files .gitignore covers\")\n    .option(\"--no-check-sources\", \"refused: update needs the sources\")\n    .option(\"--root <dir>\", \"directory src: paths resolve from (as check)\")\n    .option(\"--accept\", \"re-mint changed and never-true entries at HEAD; prints old and new pins\")\n    .option(\n      \"--recommit\",\n      \"re-record commit-sha where the recorded commit does not contain the pinned lines, or is outside HEAD's history\",\n    )\n    .option(\"--only <id>\", \"limit to entries with this id; repeatable\", collect, [])\n    .option(\"--dry-run\", \"print the diffs; write nothing\")\n    .option(\n      \"-f, --format <format>\",\n      `output: ${UPDATE_FORMATS.join(\" | \")}`,\n      \"pretty\",\n    )\n    .addHelpText(\n      \"after\",\n      [\n        \"\",\n        \"Examples:\",\n        \"  manni cite update docs/                          # rewrite moved entries\",\n        \"  manni cite update --accept --only fetch-timeout docs/limits.md\",\n        \"  manni cite update --dry-run docs/               # see the diffs first\",\n        \"  manni cite update --recommit docs/               # repair unsupported commit-sha\",\n      ].join(\"\\n\"),\n    )\n    .action(async (paths: string[], options: UpdateCliOptions, command: Command) => {\n      try {\n        const format = options.format;\n        if (!isUpdateFormat(format)) {\n          throw new CiteError(\n            `Unknown --format \"${format}\". Use ${COMMON_FORMAT_LIST}.`,\n          );\n        }\n        if (!options.checkSources) {\n          throw new CiteError(\n            \"update needs the sources: drop --no-check-sources (or `checkSources: false`).\",\n          );\n        }\n        const exts = options.ext ? splitList(options.ext) : undefined;\n        const usingStdin = paths.includes(STDIN_TOKEN);\n        const stdinContent = usingStdin ? await readStdin() : undefined;\n        const dryRun = Boolean(options.dryRun);\n        // With `-` the rewritten page owns stdout, as it does for `add -`; a\n        // dry run prints the diffs instead, so the report keeps stdout.\n        const pageToStdout = usingStdin && !dryRun;\n        const cwd = process.cwd();\n\n        const run = await runUpdate({\n          inputs: paths,\n          collection: options.collection,\n          exts,\n          exclude: options.exclude,\n          as: options.as,\n          ...configOption(options.config),\n          onConfigLoaded: reportConfig(format === \"pretty\" && !pageToStdout, cwd),\n          stdinContent,\n          allowEmpty: options.allowEmpty ? true : undefined,\n          respectGitignore: explicitFalse(options.gitignore),\n          onNotice: notice,\n          root: options.root,\n          accept: options.accept ? true : undefined,\n          recommit: options.recommit ? true : undefined,\n          only: options.only.length > 0 ? options.only : undefined,\n          dryRun,\n        });\n\n        const text =\n          format === \"json\"\n            ? renderUpdateJson(run)\n            : renderUpdatePretty(run, {\n                color: colorFor(command, process.stdout.isTTY),\n                // The diffs are the point of a dry run; a real run prints\n                // what it rewrote and leaves the file to say the rest.\n                showDiff: dryRun,\n              });\n        const stdinPage = pageToStdout ? run.pages.find((page) => page.content !== undefined) : undefined;\n        if (stdinPage?.content !== undefined) {\n          process.stdout.write(stdinPage.content);\n          process.stderr.write(`${text}\\n`);\n        } else {\n          process.stdout.write(`${text}\\n`);\n        }\n        // Exit 1 when something was skipped with an error-severity finding:\n        // work left undone, `fill`'s precedent.\n        process.exitCode = run.exitCode;\n      } catch (err) {\n        fail(err);\n      }\n    });\n\n  program\n    .command(\"remove\")\n    .description(\"Remove the named citations from the given pages, markers and all\")\n    .argument(\n      \"[paths...]\",\n      \"files, directories, or globs to remove from (use - for stdin)\",\n    )\n    .option(\n      \"--collection <name>\",\n      \"configured collection to run over; repeatable\",\n      collect,\n      [],\n    )\n    .option(\"--ext <list>\", \"comma-separated extensions for directory walks\")\n    .option(\"--exclude <glob>\", \"glob to exclude; repeatable\", collect, [])\n    .option(\"--as <format>\", \"force an input format for every input\")\n    .option(\"-c, --config <path>\", \"path to a manni config file\")\n    .option(\"--no-config\", \"ignore any discovered config file\")\n    .option(\"--allow-empty\", \"treat zero matched files as success\")\n    .option(\"--no-gitignore\", \"remove from files .gitignore covers\")\n    .option(\n      \"--only <id>\",\n      \"the entry to remove, by id or by pointer (/citations/N); required, and repeatable\",\n      collect,\n      [],\n    )\n    .option(\"--dry-run\", \"print the diffs and the report; write nothing\")\n    .option(\n      \"-f, --format <format>\",\n      `output: ${REMOVE_FORMATS.join(\" | \")}`,\n      \"pretty\",\n    )\n    .addHelpText(\n      \"after\",\n      [\n        \"\",\n        \"Examples:\",\n        \"  manni cite remove docs/limits.md --only fetch-timeout\",\n        \"  manni cite remove docs/ --only fetch-timeout --only retries --dry-run\",\n        \"  manni cite remove --collection site --only /citations/3 -f json\",\n      ].join(\"\\n\"),\n    )\n    .action(async (paths: string[], options: RemoveCliOptions, command: Command) => {\n      try {\n        const format = options.format;\n        if (!isRemoveFormat(format)) {\n          throw new CiteError(\n            `Unknown --format \"${format}\". Use ${COMMON_FORMAT_LIST}.`,\n          );\n        }\n        const exts = options.ext ? splitList(options.ext) : undefined;\n        const usingStdin = paths.includes(STDIN_TOKEN);\n        const stdinContent = usingStdin ? await readStdin() : undefined;\n        const dryRun = Boolean(options.dryRun);\n        // With `-` the rewritten page owns stdout, exactly as on `update -`.\n        const pageToStdout = usingStdin && !dryRun;\n        const cwd = process.cwd();\n\n        const run = await runRemove({\n          inputs: paths,\n          collection: options.collection,\n          exts,\n          exclude: options.exclude,\n          as: options.as,\n          ...configOption(options.config),\n          onConfigLoaded: reportConfig(format === \"pretty\" && !pageToStdout, cwd),\n          stdinContent,\n          allowEmpty: options.allowEmpty ? true : undefined,\n          respectGitignore: explicitFalse(options.gitignore),\n          onNotice: notice,\n          only: options.only,\n          dryRun,\n        });\n\n        const text =\n          format === \"json\"\n            ? renderRemoveJson(run)\n            : renderRemovePretty(run, {\n                color: colorFor(command, process.stdout.isTTY),\n                // The diffs are the point of a dry run; a real run prints\n                // what it removed and leaves the file to say the rest.\n                showDiff: dryRun,\n                dryRun,\n              });\n        const stdinPage = pageToStdout ? run.pages.find((page) => page.content !== undefined) : undefined;\n        if (stdinPage?.content !== undefined) {\n          process.stdout.write(stdinPage.content);\n          process.stderr.write(`${text}\\n`);\n        } else {\n          process.stdout.write(`${text}\\n`);\n        }\n        // Everything named was removed, or previewed: there is no exit 1.\n        process.exitCode = 0;\n      } catch (err) {\n        fail(err);\n      }\n    });\n\n  return program;\n}\n","/**\n * SARIF for `check`. Meta's renderer builds the envelope, the\n * repository-relative uris and the fingerprints the baseline shares, from the\n * adapted results. What it cannot know is what a cite rule is: it describes\n * every rule as a schema keyword, links meta's fix page, and prefixes each\n * message with the JSON Pointer of the entry, `(root)` for a finding about no\n * entry. This renderer replaces those three with the cite rule's own\n * description, a link to its row of the citations reference, and the message\n * the github annotation carries, which names the citation the pointer only\n * numbered. A message is no part of a fingerprint, so the baseline is\n * unaffected.\n */\nimport { renderSarif, type ValidationResult } from \"../../meta/index.js\";\nimport { errorSite } from \"../core/adapt.js\";\nimport { RULE_ID_PREFIX, isCiteRule } from \"../core/severity.js\";\nimport type { CheckRun, CiteRule } from \"../types.js\";\nimport { findingMessage } from \"./github.js\";\n\nconst INFORMATION_URI = \"https://hawkeyexl.github.io/manni/cite/\";\n\n/** The citations reference, whose rule tables anchor each row by rule name. */\nconst RULES_URI = \"https://hawkeyexl.github.io/manni/cite/reference/citations/\";\n\n/** What each rule is, as the citations reference's tables say it. */\nconst RULE_DESCRIPTIONS: Readonly<Record<CiteRule, string>> = {\n  \"source-moved\": \"The cited source lines moved to one other place in the file.\",\n  \"source-moved-ambiguous\": \"The cited source lines now match at several places in the file.\",\n  \"source-changed\": \"The cited source lines changed since the citation pinned them.\",\n  \"source-never-true\": \"The pin never matched the source at the recorded commit.\",\n  \"source-missing\": \"The cited source file is not tracked under the root, or cannot be decrypted.\",\n  \"claim-moved\": \"The cited sentence moved to other lines of the page.\",\n  \"claim-moved-ambiguous\": \"The cited sentence now appears at several places on the page.\",\n  \"claim-reanchored\": \"The cited sentence's words are unchanged since the claim's baseline, and only its layout moved.\",\n  \"claim-changed\": \"The cited sentence was edited since the citation pinned it.\",\n  \"marker-orphan\": \"A marker names an id no citation has.\",\n  \"marker-invalid\": \"A marker is malformed, or the page has too many markers.\",\n  \"marker-repeated\": \"Two markers name the same citation id.\",\n  \"marker-misplaced\": \"A marker line sits inside the paragraph it anchors, and splits it.\",\n  \"anchor-invalid\": \"A citation's anchor cannot work.\",\n  \"entry-invalid\": \"A citation entry is malformed.\",\n  \"quote-drift\": \"A quoted block no longer reproduces its source.\",\n};\n\n/**\n * The label meta's reporters put before a message: `(root) ` for a finding\n * about no entry, `/citations/N ` for one about an entry. Nothing else ever\n * opens a cite finding's adapted message.\n */\nexport const ENTRY_LABEL = /^(?:\\(root\\)|\\/citations\\/\\d+) /;\n\nexport interface SarifRule {\n  id: string;\n  shortDescription: { text: string };\n  helpUri?: string;\n}\n\n/** As much of meta's SARIF as this renderer and its tests read back. */\nexport interface SarifLog {\n  runs: {\n    tool: { driver: { informationUri: string; rules: SarifRule[] } };\n    results: { ruleId: string; message: { text: string } }[];\n  }[];\n}\n\n/**\n * The adapted results with each message rewritten as the github annotation\n * says it. An error is paired with its finding by rule, entry, line and\n * message, as the baseline split pairs them; the baseline has already\n * dropped the errors it forgives.\n */\nexport function withFindingMessages(run: CheckRun): ValidationResult[] {\n  return run.results.map((result) => {\n    const page = run.pages.find((p) => p.file === result.file);\n    if (page === undefined) return result;\n    const errors = result.errors.map((error) => {\n      const finding = page.findings.find(\n        (f) =>\n          f.rule === error.keyword &&\n          (f.index === undefined ? \"\" : `/citations/${String(f.index)}`) === error.instancePath &&\n          f.message === error.message &&\n          (errorSite(f).line ?? null) === (error.line ?? null),\n      );\n      return finding === undefined ? error : { ...error, message: findingMessage(finding) };\n    });\n    return { ...result, errors };\n  });\n}\n\n/** A rule as the citation tool describes it. */\nfunction describe(rule: SarifRule): SarifRule {\n  const name = rule.id.slice(RULE_ID_PREFIX.length + 1);\n  if (!isCiteRule(name)) return rule;\n  return { id: rule.id, shortDescription: { text: RULE_DESCRIPTIONS[name] }, helpUri: `${RULES_URI}#${name}` };\n}\n\nexport function renderCheckSarif(run: CheckRun, opts: { onNotice?: (message: string) => void } = {}): string {\n  const log = JSON.parse(\n    renderSarif(withFindingMessages(run), {\n      frame: run.frame,\n      ...(opts.onNotice === undefined ? {} : { onNotice: opts.onNotice }),\n    }),\n  ) as SarifLog;\n  for (const sarifRun of log.runs) {\n    sarifRun.tool.driver.informationUri = INFORMATION_URI;\n    sarifRun.tool.driver.rules = sarifRun.tool.driver.rules.map(describe);\n    for (const result of sarifRun.results) result.message.text = result.message.text.replace(ENTRY_LABEL, \"\");\n  }\n  return JSON.stringify(log, null, 2);\n}\n","/**\n * JUnit for `check`: meta's renderer over the adapted results, under the\n * `manni.cite` classname, with each failure's message the one the github\n * annotation carries.\n * Meta's renderer opens every message with the entry's JSON Pointer, `(root)`\n * for a finding about no entry, which says nothing about a citation. The\n * failure's `type` is already the rule id.\n */\nimport { renderJunit } from \"../../meta/index.js\";\nimport type { CheckRun } from \"../types.js\";\nimport { ENTRY_LABEL, withFindingMessages } from \"./sarif.js\";\n\n/** JUnit `classname` for the citation tool's findings. */\nexport const JUNIT_CLASSNAME = \"manni.cite\";\n\n/** A `message=\"` attribute's opening label. The value is escaped, so `message=\"` opens nothing else. */\nconst MESSAGE_LABEL = new RegExp(`message=\"${ENTRY_LABEL.source.replace(/^\\^/, \"\")}`, \"g\");\n\nexport function renderCheckJunit(run: CheckRun): string {\n  return renderJunit(withFindingMessages(run), { frame: run.frame, classname: JUNIT_CLASSNAME }).replace(\n    MESSAGE_LABEL,\n    'message=\"',\n  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