substrata-cli 0.1.0

package/dist/chunk-5LCVXNHI.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/index.ts","../src/wizard/prompts.ts","../src/util.ts","../src/commands/add.ts","../src/render/context.ts","../src/commands/auto-index.ts","../src/commands/context.ts","../src/commands/doctor.ts","../src/commands/hook.ts","../src/commands/index.ts","../src/commands/init.ts","../src/wizard/init-wizard.ts","../src/mcp-clients/claude-code.ts","../src/mcp-clients/json-config.ts","../src/mcp-clients/cursor.ts","../src/mcp-clients/windsurf.ts","../src/mcp-clients/registry.ts","../src/render/table.ts","../src/commands/list.ts","../src/commands/mcp.ts","../src/commands/memory-update.ts","../src/commands/search.ts","../src/commands/show.ts","../src/commands/supersede.ts"],"sourcesContent":["import { Command } from 'commander';\nimport pc from 'picocolors';\n\nimport { registerAddCommand } from './commands/add';\nimport { registerContextCommand } from './commands/context';\nimport { registerDoctorCommand } from './commands/doctor';\nimport { registerHookCommand } from './commands/hook';\nimport { registerIndexCommand } from './commands/index';\nimport { registerInitCommand } from './commands/init';\nimport { registerListCommand } from './commands/list';\nimport { registerMcpCommand } from './commands/mcp';\nimport { registerMemoryUpdateCommand } from './commands/memory-update';\nimport { registerSearchCommand } from './commands/search';\nimport { registerShowCommand } from './commands/show';\nimport { registerSupersedeCommand } from './commands/supersede';\nimport { CliError, out } from './util';\nimport { PromptCancelledError } from './wizard/prompts';\n\n/**\n * Build the commander program. Exported for tests: callers can do\n * `buildProgram().parseAsync(['node','substrata', ...])` and inject a cwd via the\n * hidden global `--cwd` option.\n *\n * Exit codes: 0 success, 1 user/expected errors (friendly, no stack), 2 unexpected.\n */\nexport function buildProgram(): Command {\n  const program = new Command();\n\n  program\n    .name('substrata')\n    .description('Shared project memory for AI engineering agents')\n    .version('0.1.0')\n    // Hidden global flag so tests can run commands against a temp dir.\n    .option('--cwd <dir>', 'Run as if invoked from this directory')\n    .enablePositionalOptions();\n\n  // Don't let commander call process.exit() during tests/embedding.\n  program.exitOverride();\n\n  registerInitCommand(program);\n  registerAddCommand(program);\n  registerSearchCommand(program);\n  registerContextCommand(program);\n  registerIndexCommand(program);\n  registerListCommand(program);\n  registerShowCommand(program);\n  registerDoctorCommand(program);\n  registerSupersedeCommand(program);\n  registerMemoryUpdateCommand(program);\n  registerHookCommand(program);\n  registerMcpCommand(program);\n\n  return program;\n}\n\n/** Map an unknown error to an exit code, printing a friendly message. */\nfunction reportError(err: unknown): number {\n  if (err instanceof CliError) {\n    out.err(err.message);\n    return err.exitCode;\n  }\n  if (err instanceof PromptCancelledError) {\n    out.info('Cancelled.');\n    return 1;\n  }\n  // Commander throws CommanderError for help/version/parse issues.\n  const e = err as { code?: string; exitCode?: number; message?: string };\n  if (e && typeof e.code === 'string' && e.code.startsWith('commander.')) {\n    // help/version are not failures.\n    if (e.code === 'commander.helpDisplayed' || e.code === 'commander.version') return 0;\n    if (e.message) out.err(e.message);\n    return typeof e.exitCode === 'number' ? e.exitCode : 1;\n  }\n  // Unexpected: surface the message without a stack, exit 2.\n  out.err(`Unexpected error: ${(err as Error)?.message ?? String(err)}`);\n  process.stderr.write(`${pc.dim('This is a bug — please file an issue.')}\\n`);\n  return 2;\n}\n\n/** Parse argv and run. Returns the process exit code (does not call exit). */\nexport async function runCli(argv: string[]): Promise<number> {\n  const program = buildProgram();\n  try {\n    await program.parseAsync(argv);\n    return Number(process.exitCode ?? 0);\n  } catch (err) {\n    return reportError(err);\n  }\n}\n","import {\n  confirm as clackConfirm,\n  isCancel,\n  multiselect as clackMultiselect,\n  text as clackText,\n  type Option,\n} from '@clack/prompts';\n\n/**\n * Thin wrapper over @clack/prompts with a non-TTY guard.\n *\n * When stdout/stdin is not a TTY, or `assumeYes` is set, prompts must NOT render;\n * every prompt resolves to its supplied default. This keeps the wizard usable in\n * pipes/CI (which behave as `--yes`) and in tests without a fake terminal.\n */\n\nlet assumeYesFlag = false;\n\n/** Force non-interactive mode (used by `--yes` and non-TTY detection). */\nexport function setAssumeYes(value: boolean): void {\n  assumeYesFlag = value;\n}\n\n/** True when prompts should be skipped (non-TTY or `--yes`). */\nexport function isNonInteractive(): boolean {\n  return assumeYesFlag || !process.stdout.isTTY || !process.stdin.isTTY;\n}\n\n/** Raised when a user cancels an interactive prompt (Ctrl-C). */\nexport class PromptCancelledError extends Error {\n  constructor() {\n    super('Prompt cancelled');\n    this.name = 'PromptCancelledError';\n  }\n}\n\nfunction guardCancel<T>(value: T | symbol): T {\n  if (isCancel(value)) throw new PromptCancelledError();\n  return value as T;\n}\n\n/** Free-text prompt. Returns `defaultValue` in non-interactive mode. */\nexport async function promptText(options: {\n  message: string;\n  defaultValue: string;\n  placeholder?: string;\n}): Promise<string> {\n  if (isNonInteractive()) return options.defaultValue;\n  const result = await clackText({\n    message: options.message,\n    placeholder: options.placeholder ?? options.defaultValue,\n    defaultValue: options.defaultValue,\n    initialValue: options.defaultValue,\n  });\n  const value = guardCancel(result);\n  return value.length > 0 ? value : options.defaultValue;\n}\n\n/** Yes/no prompt. Returns `defaultValue` in non-interactive mode. */\nexport async function promptConfirm(options: {\n  message: string;\n  defaultValue: boolean;\n}): Promise<boolean> {\n  if (isNonInteractive()) return options.defaultValue;\n  const result = await clackConfirm({\n    message: options.message,\n    initialValue: options.defaultValue,\n  });\n  return guardCancel(result);\n}\n\n/** Multi-select prompt. Returns `defaultValues` in non-interactive mode. */\nexport async function promptMultiselect<Value>(options: {\n  message: string;\n  choices: Array<{ value: Value; label: string; hint?: string }>;\n  defaultValues: Value[];\n}): Promise<Value[]> {\n  if (isNonInteractive()) return options.defaultValues;\n  if (options.choices.length === 0) return [];\n  // `Option<Value>` is a conditional type; an unresolved generic can't be\n  // simplified by TS, so build the array as the concrete shape and assert.\n  const choices = options.choices.map((c) => ({\n    value: c.value,\n    label: c.label,\n    ...(c.hint !== undefined ? { hint: c.hint } : {}),\n  })) as Option<Value>[];\n\n  const result = await clackMultiselect<Value>({\n    message: options.message,\n    options: choices,\n    initialValues: options.defaultValues,\n    required: false,\n  });\n  return guardCancel(result);\n}\n","import { execFile } from 'node:child_process';\nimport { promisify } from 'node:util';\n\nimport { loadConfig, type SubstrataConfig } from '@substrata/core';\nimport pc from 'picocolors';\n\n/**\n * Shared CLI helpers: cwd resolution, git shell-outs, attribution precedence,\n * and a typed error class for friendly (exit 1) failures.\n */\n\nconst execFileAsync = promisify(execFile);\n\n/** A user/expected error: printed as a friendly message, no stack, exit code 1. */\nexport class CliError extends Error {\n  readonly exitCode: number;\n  constructor(message: string, exitCode = 1) {\n    super(message);\n    this.name = 'CliError';\n    this.exitCode = exitCode;\n  }\n}\n\n/** Resolve the working directory from the hidden global `--cwd` option. */\nexport function resolveCwd(opts: { cwd?: string } | undefined): string {\n  return opts?.cwd ? opts.cwd : process.cwd();\n}\n\nexport const out = {\n  ok: (msg: string) => process.stdout.write(`${pc.green('✔')} ${msg}\\n`),\n  info: (msg: string) => process.stdout.write(`${pc.blue('ℹ')} ${msg}\\n`),\n  warn: (msg: string) => process.stderr.write(`${pc.yellow('!')} ${msg}\\n`),\n  err: (msg: string) => process.stderr.write(`${pc.red('✖')} ${msg}\\n`),\n  plain: (msg: string) => process.stdout.write(`${msg}\\n`),\n};\n\n/** Run a git command in `cwd`; returns trimmed stdout or null on failure. */\nexport async function git(cwd: string, args: string[]): Promise<string | null> {\n  try {\n    const { stdout } = await execFileAsync('git', args, { cwd });\n    return stdout.trim();\n  } catch {\n    return null;\n  }\n}\n\n/** True if `cwd` is inside a git work tree. */\nexport async function isGitRepo(cwd: string): Promise<boolean> {\n  const result = await git(cwd, ['rev-parse', '--is-inside-work-tree']);\n  return result === 'true';\n}\n\nexport type GitContext = {\n  branch?: string;\n  files: string[];\n  commit?: string;\n};\n\n/** Collect branch, changed files (staged + unstaged), and HEAD commit. */\nexport async function collectGitContext(cwd: string): Promise<GitContext> {\n  const branch = (await git(cwd, ['rev-parse', '--abbrev-ref', 'HEAD'])) ?? undefined;\n  const commit = (await git(cwd, ['rev-parse', 'HEAD'])) ?? undefined;\n\n  const staged = await git(cwd, ['diff', '--cached', '--name-only']);\n  const unstaged = await git(cwd, ['diff', '--name-only']);\n  const files = new Set<string>();\n  for (const block of [staged, unstaged]) {\n    if (!block) continue;\n    for (const line of block.split(/\\r?\\n/)) {\n      const t = line.trim();\n      if (t.length > 0) files.add(t);\n    }\n  }\n\n  return {\n    branch: branch && branch !== 'HEAD' ? branch : undefined,\n    files: Array.from(files),\n    commit,\n  };\n}\n\nexport type Attribution = {\n  actor: string;\n  model?: string;\n  requester?: string;\n};\n\n/**\n * Resolve actor / model / requester by the precedence in plan §8.2.\n *   actor:     --actor → $SUBSTRATA_ACTOR → config.agent.default_actor → \"unknown-agent\"\n *   model:     --model → $SUBSTRATA_MODEL → config.agent.default_model → omit\n *   requester: --requester → $SUBSTRATA_REQUESTER → git user.email → omit\n */\nexport async function resolveAttribution(\n  cwd: string,\n  config: SubstrataConfig,\n  flags: { actor?: string; model?: string; requester?: string },\n): Promise<Attribution> {\n  const env = process.env;\n\n  const actor = flags.actor || env.SUBSTRATA_ACTOR || config.agent.default_actor || 'unknown-agent';\n\n  const model = flags.model || env.SUBSTRATA_MODEL || config.agent.default_model || undefined;\n\n  let requester = flags.requester || env.SUBSTRATA_REQUESTER || undefined;\n  if (!requester) {\n    const email = await git(cwd, ['config', 'user.email']);\n    if (email) requester = email;\n  }\n\n  return { actor, model, requester };\n}\n\n/** Load config, mapping a missing/invalid config to a friendly CliError. */\nexport async function requireConfig(cwd: string): Promise<SubstrataConfig> {\n  try {\n    return await loadConfig(cwd);\n  } catch (err) {\n    throw new CliError(\n      `${(err as Error).message}\\nRun \\`substrata init\\` to set up this repository.`,\n    );\n  }\n}\n","import {\n  SecretDetectedError,\n  supersedeFootprint,\n  writeFootprint,\n  type RejectedOption,\n  type WorkType,\n  type WriteFootprintInput,\n} from '@substrata/core';\nimport type { Command } from 'commander';\n\nimport { promptText, isNonInteractive } from '../wizard/prompts';\nimport {\n  CliError,\n  collectGitContext,\n  out,\n  requireConfig,\n  resolveAttribution,\n  resolveCwd,\n} from '../util';\n\n/**\n * `substrata add` — create a footprint, interactive or non-interactive. Resolves\n * actor/model/requester by precedence (plan §8.2), optionally enriches from Git\n * (`--from-git`), runs the secret scan inside core (catching SecretDetectedError\n * to print the §12 refusal), and prints the §12 commit reminder on success.\n */\n\nconst SECURITY_REMINDER =\n  'Reminder: Substrata files are intended to be committed.\\n' +\n  'Do not include secrets, credentials, or sensitive user data.';\n\ntype AddOptions = {\n  title?: string;\n  purpose?: string;\n  actor?: string;\n  requester?: string;\n  model?: string;\n  files?: string;\n  tag?: string[];\n  workType?: string;\n  decision?: string[];\n  rejected?: string[];\n  notes?: string;\n  memory?: string[];\n  guidance?: string;\n  template?: string;\n  supersedes?: string;\n  allowSecret?: boolean;\n  fromGit?: boolean;\n};\n\nfunction collect(value: string, previous: string[] = []): string[] {\n  return [...previous, value];\n}\n\nfunction splitCsv(value: string | undefined): string[] {\n  if (!value) return [];\n  return value\n    .split(',')\n    .map((s) => s.trim())\n    .filter((s) => s.length > 0);\n}\n\n/** Parse a `--rejected \"option:reason\"` value into a structured RejectedOption. */\nfunction parseRejected(values: string[] | undefined): RejectedOption[] {\n  if (!values) return [];\n  return values.map((v) => {\n    const idx = v.indexOf(':');\n    if (idx === -1) return { option: v.trim(), reason: '' };\n    return { option: v.slice(0, idx).trim(), reason: v.slice(idx + 1).trim() };\n  });\n}\n\nconst VALID_WORK_TYPES: ReadonlySet<string> = new Set<WorkType>([\n  'implementation',\n  'implementation_decision',\n  'bug_fix',\n  'refactor',\n  'investigation',\n  'architecture_decision',\n  'test_update',\n  'documentation',\n]);\n\nexport function registerAddCommand(program: Command): void {\n  program\n    .command('add')\n    .description('Create a new footprint')\n    .option('--title <title>', 'Footprint title')\n    .option('--purpose <text>', 'Why this work was done')\n    .option('--actor <id>', 'Agent that performed the work')\n    .option('--requester <id>', 'Who requested the work')\n    .option('--model <id>', 'Agent model identifier')\n    .option('--files <csv>', 'Comma-separated files touched')\n    .option('--tag <tag>', 'Tag (repeatable)', collect, [])\n    .option('--work-type <type>', 'Footprint work type')\n    .option('--decision <text>', 'Decision made (repeatable)', collect, [])\n    .option('--rejected <option:reason>', 'Rejected option (repeatable)', collect, [])\n    .option('--notes <text>', 'Implementation notes')\n    .option('--memory <text>', 'Memory learned (repeatable)', collect, [])\n    .option('--guidance <text>', 'Future agent guidance')\n    .option('--template <type>', 'Work type template to seed the footprint')\n    .option('--supersedes <id>', 'Mark this footprint as superseding an old one')\n    .option('--allow-secret', 'Write even if a secret is detected (NOT recommended)')\n    .option('--from-git', 'Populate branch/files/commit from Git')\n    .action(async (opts: AddOptions, command: Command) => {\n      const cwd = resolveCwd(command.parent?.opts());\n      const config = await requireConfig(cwd);\n\n      const attribution = await resolveAttribution(cwd, config, {\n        actor: opts.actor,\n        model: opts.model,\n        requester: opts.requester,\n      });\n\n      // Title: required in non-interactive mode; prompted otherwise.\n      let title = opts.title;\n      if (!title) {\n        if (isNonInteractive()) {\n          throw new CliError('`--title` is required in non-interactive mode.');\n        }\n        title = await promptText({ message: 'Title', defaultValue: '' });\n        if (!title.trim()) throw new CliError('A title is required.');\n      }\n\n      const purpose =\n        opts.purpose ??\n        (isNonInteractive()\n          ? undefined\n          : (await promptText({ message: 'Purpose', defaultValue: '' })) || undefined);\n\n      const workTypeRaw = opts.workType ?? opts.template;\n      if (workTypeRaw && !VALID_WORK_TYPES.has(workTypeRaw)) {\n        throw new CliError(\n          `Invalid work type \"${workTypeRaw}\". Valid: ${Array.from(VALID_WORK_TYPES).join(', ')}.`,\n        );\n      }\n      const workType = workTypeRaw as WorkType | undefined;\n\n      let filesTouched = splitCsv(opts.files);\n      let repoBranch: string | undefined;\n      let commits: string[] | undefined;\n\n      if (opts.fromGit) {\n        const ctx = await collectGitContext(cwd);\n        repoBranch = ctx.branch;\n        if (ctx.files.length > 0) {\n          filesTouched = Array.from(new Set([...filesTouched, ...ctx.files]));\n        }\n        if (ctx.commit) commits = [ctx.commit];\n      }\n\n      const supersedes = opts.supersedes ? [opts.supersedes] : undefined;\n\n      const input: WriteFootprintInput & { cwd: string } = {\n        cwd,\n        title,\n        purpose,\n        actor: attribution.actor,\n        requester: attribution.requester,\n        agentModel: attribution.model,\n        workType,\n        decisions: opts.decision && opts.decision.length > 0 ? opts.decision : undefined,\n        rejectedOptions:\n          opts.rejected && opts.rejected.length > 0 ? parseRejected(opts.rejected) : undefined,\n        implementationNotes: opts.notes,\n        memoryLearned: opts.memory && opts.memory.length > 0 ? opts.memory : undefined,\n        futureAgentGuidance: opts.guidance,\n        filesTouched: filesTouched.length > 0 ? filesTouched : undefined,\n        tags: opts.tag && opts.tag.length > 0 ? opts.tag : undefined,\n        repo: repoBranch ? { branch: repoBranch } : undefined,\n        related: commits ? { commits } : undefined,\n        supersedes,\n        allowSecret: opts.allowSecret,\n      };\n\n      let footprint;\n      try {\n        footprint = await writeFootprint(input);\n      } catch (err) {\n        if (err instanceof SecretDetectedError) {\n          // §12 refusal: print pattern names + line numbers, NEVER values.\n          const detail = err.findings.map((f) => `  - ${f.name} at body line ${f.line}`).join('\\n');\n          throw new CliError(\n            `Refusing to write footprint: ${err.findings.length} potential secret(s) detected\\n${detail}\\n` +\n              '  Redact these or pass --allow-secret to override (NOT recommended — footprints are committed).',\n          );\n        }\n        throw err;\n      }\n\n      // If superseding, also flip the old footprint's status/links.\n      if (opts.supersedes) {\n        await supersedeFootprint(cwd, opts.supersedes, footprint.frontmatter.id);\n      }\n\n      out.ok(`Footprint written: ${footprint.frontmatter.id}`);\n      out.plain(`  ${footprint.filePath}`);\n      out.warn(SECURITY_REMINDER);\n    });\n}\n","import type { Footprint, MemoryDocument, SearchResult } from '@substrata/core';\n\n/**\n * Build the LLM-friendly `context` output (plan §8.4). Each ranked source is\n * rendered as a numbered point with a one-line statement, an optional Reason,\n * and a Source: path. Sources are added in ranked order until adding the next\n * one would exceed the token budget.\n *\n * Token budget is a documented character approximation: `ceil(chars / 3.5)`.\n * No real tokenizer is bundled (plan §8.4). We round up so the estimate\n * under-fills rather than overflows.\n */\n\nconst CHARS_PER_TOKEN = 3.5;\n\n/** Approximate token count for a string (ceil(chars / 3.5)). */\nexport function estimateTokens(text: string): number {\n  return Math.ceil(text.length / CHARS_PER_TOKEN);\n}\n\nexport type ContextSource = {\n  id: string;\n  title: string;\n  filePath: string;\n};\n\nexport type ContextResult = {\n  text: string;\n  sources: ContextSource[];\n};\n\nconst HEADER = 'Relevant Substrata context:';\nconst APPROX_NOTE = '(Token counts are approximate — estimated, not tokenizer-exact.)';\n\n/** First non-empty line of a block of text, trimmed. */\nfunction firstLine(text: string | undefined): string | undefined {\n  if (!text) return undefined;\n  for (const line of text.split(/\\r?\\n/)) {\n    const t = line.trim();\n    if (t.length > 0) return t;\n  }\n  return undefined;\n}\n\n/**\n * Derive a concise statement + optional reason for a footprint, preferring the\n * most decision-bearing section available.\n */\nfunction footprintPoint(fp: Footprint): { statement: string; reason?: string } {\n  const s = fp.sections;\n  if (s.decisions && s.decisions.length > 0) {\n    const rejected = s.rejectedOptions?.[0];\n    return {\n      statement: s.decisions[0]!,\n      reason: rejected ? `${rejected.option} was rejected — ${rejected.reason}` : undefined,\n    };\n  }\n  if (s.rejectedOptions && s.rejectedOptions.length > 0) {\n    const r = s.rejectedOptions[0]!;\n    return { statement: `Avoid ${r.option} for ${fp.title}.`, reason: r.reason };\n  }\n  if (s.futureAgentGuidance) {\n    return { statement: firstLine(s.futureAgentGuidance) ?? fp.title };\n  }\n  if (s.purpose) {\n    return { statement: fp.title, reason: firstLine(s.purpose) };\n  }\n  return { statement: fp.title };\n}\n\n/** Derive a concise statement for a memory document (first bullet or title). */\nfunction memoryPoint(doc: MemoryDocument): { statement: string } {\n  for (const line of doc.body.split(/\\r?\\n/)) {\n    const t = line.trim();\n    if (t.startsWith('- ')) return { statement: t.slice(2).trim() };\n  }\n  return { statement: doc.title };\n}\n\ntype Resolved = { source: ContextSource; block: string };\n\nfunction blockFor(\n  result: SearchResult,\n  footprintsById: Map<string, Footprint>,\n  memoryById: Map<string, MemoryDocument>,\n  index: number,\n): Resolved {\n  const fp = footprintsById.get(result.id);\n  const mem = memoryById.get(result.id);\n\n  let statement: string;\n  let reason: string | undefined;\n  if (fp) {\n    ({ statement, reason } = footprintPoint(fp));\n  } else if (mem) {\n    ({ statement } = memoryPoint(mem));\n  } else {\n    statement = result.title || result.id;\n  }\n\n  const lines = [`${index}. ${statement}`];\n  if (reason) lines.push(`   Reason: ${reason}`);\n  lines.push(`   Source: ${result.filePath}`);\n\n  return {\n    source: { id: result.id, title: result.title, filePath: result.filePath },\n    block: lines.join('\\n'),\n  };\n}\n\n/**\n * Render ranked results into the LLM-friendly context string within a token\n * budget. Adds sources in order until the next would overflow `maxTokens`.\n */\nexport function renderContext(\n  results: SearchResult[],\n  footprints: Footprint[],\n  memory: MemoryDocument[],\n  maxTokens: number,\n): ContextResult {\n  const footprintsById = new Map(footprints.map((f) => [f.frontmatter.id, f]));\n  const memoryById = new Map(memory.map((m) => [m.frontmatter.id, m]));\n\n  const header = `${HEADER}\\n\\n`;\n  const footer = `\\n\\n${APPROX_NOTE}`;\n  let used = estimateTokens(header) + estimateTokens(footer);\n\n  const chosen: ContextSource[] = [];\n  const blocks: string[] = [];\n\n  let n = 1;\n  for (const result of results) {\n    const { source, block } = blockFor(result, footprintsById, memoryById, n);\n    const blockTokens = estimateTokens(`${block}\\n\\n`);\n    if (used + blockTokens > maxTokens && blocks.length > 0) break;\n    blocks.push(block);\n    chosen.push(source);\n    used += blockTokens;\n    n += 1;\n  }\n\n  if (blocks.length === 0) {\n    return { text: `${HEADER}\\n\\nNo relevant context found.`, sources: [] };\n  }\n\n  return { text: `${header}${blocks.join('\\n\\n')}${footer}`, sources: chosen };\n}\n","import { buildIndex, getIndexStatus } from '@substrata/search';\n\nimport { out } from '../util';\n\n/**\n * Shared lazy-index helper for `search` and `context` (plan §8.3/§8.5). Rebuilds\n * a missing or stale index unless `--no-auto-index` was passed. A freshly cloned\n * repo (no index/) \"just works\" on the first query.\n */\nexport async function ensureFreshIndex(cwd: string, autoIndex: boolean): Promise<void> {\n  const status = await getIndexStatus(cwd);\n  if (status.state === 'fresh') return;\n\n  if (!autoIndex) {\n    out.info(\n      status.state === 'missing'\n        ? 'Index missing — run `substrata index` (auto-index disabled).'\n        : `Index stale (${status.reason}) — run \\`substrata index\\` (auto-index disabled).`,\n    );\n    return;\n  }\n\n  await buildIndex(cwd);\n}\n","import { listFootprints, listMemoryDocuments } from '@substrata/core';\nimport { search } from '@substrata/search';\nimport type { Command } from 'commander';\n\nimport { renderContext } from '../render/context';\nimport { out, requireConfig, resolveCwd } from '../util';\n\nimport { ensureFreshIndex } from './auto-index';\n\n/**\n * `substrata context <task>` — concise, source-linked context for an agent\n * before work begins. Excludes superseded footprints by DEFAULT (agents should\n * see the current decision). Fits a token budget estimated as ceil(chars/3.5).\n * Auto-(re)builds a stale/missing index like `search` (plan §8.4).\n */\n\ntype ContextOptions = {\n  json?: boolean;\n  maxTokens?: string;\n  files?: string[];\n  autoIndex?: boolean;\n};\n\nfunction collect(value: string, previous: string[] = []): string[] {\n  return [...previous, value];\n}\n\nexport function registerContextCommand(program: Command): void {\n  program\n    .command('context <task>')\n    .description('Return concise, source-linked context for an agent')\n    .option('--json', 'Output JSON ({ context, sources })')\n    .option('--max-tokens <n>', 'Approximate token budget (chars/3.5)')\n    .option('--files <path>', 'Bias toward docs touching this file (repeatable)', collect, [])\n    .option('--no-auto-index', 'Do not auto-(re)build a stale/missing index')\n    .action(async (task: string, opts: ContextOptions, command: Command) => {\n      const cwd = resolveCwd(command.parent?.opts());\n      const config = await requireConfig(cwd);\n\n      await ensureFreshIndex(cwd, opts.autoIndex !== false);\n\n      const maxTokens = opts.maxTokens ? Number(opts.maxTokens) : config.search.max_context_tokens;\n      const budget = Number.isFinite(maxTokens) ? maxTokens : config.search.max_context_tokens;\n\n      const results = await search(task, {\n        cwd,\n        limit: config.search.default_limit,\n        files: opts.files && opts.files.length > 0 ? opts.files : undefined,\n        excludeSuperseded: true,\n      });\n\n      const [footprints, memory] = await Promise.all([\n        listFootprints(cwd),\n        listMemoryDocuments(cwd),\n      ]);\n\n      const rendered = renderContext(results, footprints, memory, budget);\n\n      if (opts.json) {\n        out.plain(JSON.stringify({ context: rendered.text, sources: rendered.sources }, null, 2));\n        return;\n      }\n      out.plain(rendered.text);\n    });\n}\n","import { existsSync, readFileSync } from 'node:fs';\nimport path from 'node:path';\n\nimport {\n  GITIGNORE_LINES,\n  listFootprints,\n  listMemoryDocuments,\n  loadConfig,\n  substrataDir,\n} from '@substrata/core';\nimport { getIndexStatus } from '@substrata/search';\nimport type { Command } from 'commander';\n\nimport { out, resolveCwd } from '../util';\n\n/**\n * `substrata doctor` — health check (plan §8.8). A missing/stale index is\n * informational (ℹ), not an error. Non-zero exit only for: invalid config,\n * unparseable footprint/memory files, or a gitignore that would commit the DB.\n *\n * Returns the number of hard failures so the program can set the exit code.\n */\nexport async function runDoctor(cwd: string): Promise<number> {\n  let failures = 0;\n\n  // .substrata exists\n  if (existsSync(substrataDir(cwd))) {\n    out.ok('.substrata exists');\n  } else {\n    out.err('.substrata missing — run `substrata init`');\n    return 1;\n  }\n\n  // config valid\n  try {\n    await loadConfig(cwd);\n    out.ok('config valid');\n  } catch (err) {\n    out.err(`config invalid: ${(err as Error).message}`);\n    failures += 1;\n  }\n\n  // index status (informational only)\n  const status = await getIndexStatus(cwd);\n  if (status.state === 'fresh') {\n    out.ok('index fresh');\n  } else if (status.state === 'missing') {\n    out.info('index missing — run `substrata index` (or it builds automatically on first search)');\n  } else {\n    out.info(`index stale (${status.reason}) — run \\`substrata index\\``);\n  }\n\n  // gitignore covers index/ and cache/ (else the generated DB would be committed)\n  const gitignorePath = path.join(cwd, '.gitignore');\n  const gitignore = existsSync(gitignorePath) ? readFileSync(gitignorePath, 'utf8') : '';\n  const ignoredLines = new Set(gitignore.split(/\\r?\\n/).map((l) => l.trim()));\n  const indexCovered = ignoredLines.has('.substrata/index/') || ignoredLines.has('.substrata/');\n  if (indexCovered) {\n    out.ok('gitignore covers index/ and cache/');\n  } else {\n    out.err(`gitignore would commit the generated DB — add: ${GITIGNORE_LINES.join(', ')}`);\n    failures += 1;\n  }\n\n  // footprints parse\n  try {\n    const footprints = await listFootprints(cwd);\n    out.ok(`${footprints.length} footprint file(s) parsed`);\n  } catch (err) {\n    out.err(`footprint parse error: ${(err as Error).message}`);\n    failures += 1;\n  }\n\n  // memory parses\n  try {\n    const memory = await listMemoryDocuments(cwd);\n    out.ok(`${memory.length} memory file(s) parsed`);\n  } catch (err) {\n    out.err(`memory parse error: ${(err as Error).message}`);\n    failures += 1;\n  }\n\n  return failures;\n}\n\nexport function registerDoctorCommand(program: Command): void {\n  program\n    .command('doctor')\n    .description('Check repository setup')\n    .action(async (_opts: unknown, command: Command) => {\n      const cwd = resolveCwd(command.parent?.opts());\n      const failures = await runDoctor(cwd);\n      if (failures > 0) {\n        process.exitCode = 1;\n      }\n    });\n}\n","import { readFile } from 'node:fs/promises';\nimport path from 'node:path';\n\nimport { installSecretHook, scanForSecrets } from '@substrata/core';\nimport type { Command } from 'commander';\n\nimport { git, out, resolveCwd } from '../util';\n\n/**\n * `substrata hook install` — install the pre-commit secret hook (plan §8.11).\n * `substrata hook run` (and the internal `internal-scan-staged` alias the hook\n * script invokes) — scan staged `.substrata` files and exit 1 on findings.\n */\n\n/**\n * Scan staged `.substrata/**` files for secrets. Returns the number of files\n * with findings (0 = clean). Prints pattern names + line numbers, never values.\n */\nasync function scanStaged(cwd: string): Promise<number> {\n  const staged = await git(cwd, ['diff', '--cached', '--name-only']);\n  if (!staged) return 0;\n\n  const files = staged\n    .split(/\\r?\\n/)\n    .map((l) => l.trim())\n    .filter((l) => l.startsWith('.substrata/') && l.endsWith('.md'));\n\n  let flagged = 0;\n  for (const rel of files) {\n    let content: string;\n    try {\n      content = await readFile(path.join(cwd, rel), 'utf8');\n    } catch {\n      continue;\n    }\n    const findings = scanForSecrets(content);\n    if (findings.length > 0) {\n      flagged += 1;\n      out.err(`${findings.length} potential secret(s) in ${rel}:`);\n      for (const f of findings) out.plain(`  - ${f.name} at line ${f.line}`);\n    }\n  }\n  return flagged;\n}\n\nexport function registerHookCommand(program: Command): void {\n  const hook = program.command('hook').description('Pre-commit secret hook utilities');\n\n  hook\n    .command('install')\n    .description('Install the pre-commit secret scan hook')\n    .action(async (_opts: unknown, command: Command) => {\n      const cwd = resolveCwd(command.parent?.parent?.opts());\n      const result = installSecretHook(cwd);\n      if (result.action === 'skip') {\n        out.info('Pre-commit hook already installed.');\n      } else {\n        out.ok(`Pre-commit hook ${result.action === 'create' ? 'installed' : 'updated'}.`);\n      }\n    });\n\n  hook\n    .command('run')\n    .description('Scan staged .substrata files for secrets')\n    .action(async (_opts: unknown, command: Command) => {\n      const cwd = resolveCwd(command.parent?.parent?.opts());\n      const flagged = await scanStaged(cwd);\n      if (flagged > 0) process.exitCode = 1;\n    });\n\n  // The installed hook script invokes this name directly.\n  program\n    .command('internal-scan-staged', { hidden: true })\n    .action(async (_opts: unknown, command: Command) => {\n      const cwd = resolveCwd(command.parent?.opts());\n      const flagged = await scanStaged(cwd);\n      if (flagged > 0) process.exitCode = 1;\n    });\n}\n","import { buildIndex } from '@substrata/search';\nimport type { Command } from 'commander';\n\nimport { out, requireConfig, resolveCwd } from '../util';\n\n/**\n * `substrata index` / `index --rebuild` — build or rebuild the local FTS index.\n * The MVP indexer always does a full rebuild, so `--rebuild` is accepted for\n * symmetry with the documented flag.\n */\nexport function registerIndexCommand(program: Command): void {\n  program\n    .command('index')\n    .description('Build or rebuild the local search index')\n    .option('--rebuild', 'Force a full rebuild of the index')\n    .action(async (_opts: { rebuild?: boolean }, command: Command) => {\n      const cwd = resolveCwd(command.parent?.opts());\n      await requireConfig(cwd);\n      await buildIndex(cwd, { rebuild: true });\n      out.ok('Index built.');\n    });\n}\n","import { readFile, writeFile } from 'node:fs/promises';\n\nimport { configPath } from '@substrata/core';\nimport { buildIndex } from '@substrata/search';\nimport type { Command } from 'commander';\n\nimport { printResolvedConfig, runInitWizard, type InitFlags } from '../wizard/init-wizard';\nimport { setAssumeYes } from '../wizard/prompts';\nimport { out, resolveCwd } from '../util';\n\nimport { runDoctor } from './doctor';\n\n/**\n * `substrata init` — one-command setup wizard (plan §8.1). Non-TTY/`--yes`\n * accepts all defaults. After applying, runs the embedded doctor health check and\n * builds the initial index (unless `--no-index`).\n */\n\n/** Disable redaction in the written config when `--no-redact` was passed. */\nasync function disableRedaction(cwd: string): Promise<void> {\n  const file = configPath(cwd);\n  let raw: string;\n  try {\n    raw = await readFile(file, 'utf8');\n  } catch {\n    return;\n  }\n  const next = raw\n    .replace(/^(\\s*)redact:\\s*true\\s*$/m, '$1redact: false')\n    .replace(/^(\\s*)scan_content:\\s*true\\s*$/m, '$1scan_content: false')\n    .replace(/^(\\s*)block_on_secret:\\s*true\\s*$/m, '$1block_on_secret: false');\n  if (next !== raw) await writeFile(file, next, 'utf8');\n}\n\nexport function registerInitCommand(program: Command): void {\n  program\n    .command('init')\n    .description('Set up Substrata in this repository (interactive wizard)')\n    .option('--yes', 'Accept all defaults, no prompts')\n    .option('--project <name>', 'Project name')\n    .option('--actor <id>', 'Default actor')\n    .option('--model <id>', 'Default agent model')\n    .option('--requester <id>', 'Default requester')\n    .option('--no-env', \"Don't touch shell rc; print snippet instead\")\n    .option('--no-agents-md', 'Skip AGENTS.md')\n    .option('--no-mcp', 'Skip MCP registration')\n    .option('--mcp-client <name>', 'Register only this client (repeatable)', collect, [])\n    .option('--no-gitignore', \"Don't edit .gitignore\")\n    .option('--no-redact', 'Disable security redaction (NOT recommended)')\n    .option('--with-hook', 'Install the pre-commit secret hook')\n    .option('--no-index', 'Skip building the initial index')\n    .option('--print-config', 'Print resolved config.yml without writing anything')\n    .action(async (opts: InitCommandOptions, command: Command) => {\n      const cwd = resolveCwd(command.parent?.opts());\n\n      const flags: InitFlags = {\n        yes: opts.yes,\n        project: opts.project,\n        actor: opts.actor,\n        model: opts.model,\n        requester: opts.requester,\n        env: opts.env,\n        agentsMd: opts.agentsMd,\n        mcp: opts.mcp,\n        mcpClient: opts.mcpClient,\n        gitignore: opts.gitignore,\n        redact: opts.redact,\n        withHook: opts.withHook,\n        index: opts.index,\n        printConfig: opts.printConfig,\n      };\n\n      if (flags.printConfig) {\n        printResolvedConfig(cwd, flags);\n        return;\n      }\n\n      // Non-TTY contexts behave as --yes (handled inside the prompt wrapper too).\n      if (flags.yes) setAssumeYes(true);\n\n      const result = await runInitWizard(cwd, flags);\n      if (result.aborted) return;\n\n      if (flags.redact === false) {\n        await disableRedaction(cwd);\n        out.warn('Security redaction disabled (--no-redact).');\n      }\n\n      // Embedded health check (doctor logic).\n      out.plain('');\n      await runDoctor(cwd);\n\n      // Build the initial index unless skipped.\n      if (flags.index !== false) {\n        await buildIndex(cwd);\n        out.ok('Initial index built.');\n      }\n    });\n}\n\ntype InitCommandOptions = {\n  yes?: boolean;\n  project?: string;\n  actor?: string;\n  model?: string;\n  requester?: string;\n  env?: boolean;\n  agentsMd?: boolean;\n  mcp?: boolean;\n  mcpClient?: string[];\n  gitignore?: boolean;\n  redact?: boolean;\n  withHook?: boolean;\n  index?: boolean;\n  printConfig?: boolean;\n};\n\nfunction collect(value: string, previous: string[] = []): string[] {\n  return [...previous, value];\n}\n","import { existsSync, readFileSync } from 'node:fs';\nimport { homedir } from 'node:os';\nimport path from 'node:path';\n\nimport {\n  ensureGitignore,\n  initProject,\n  installSecretHook,\n  renderConfig,\n  upsertAgentsMd,\n  writeShellEnv,\n  type AttributionEnv,\n  type ChangeResult,\n} from '@substrata/core';\nimport pc from 'picocolors';\n\nimport {\n  detectMcpClients,\n  getMcpClient,\n  SUBSTRATA_MCP_SPEC,\n  type McpClient,\n} from '../mcp-clients/registry';\nimport { git, isGitRepo, out } from '../util';\n\nimport { promptConfirm, promptMultiselect, promptText } from './prompts';\n\n/**\n * The `init` setup wizard (plan §8.1). Collects answers, prints a change plan,\n * and applies nothing until one final confirmation. Idempotent: re-running enters\n * update mode (markers replaced in place; gitignore/MCP de-duplicated).\n */\n\nexport type InitFlags = {\n  yes?: boolean;\n  project?: string;\n  actor?: string;\n  model?: string;\n  requester?: string;\n  env?: boolean; // --no-env => false\n  agentsMd?: boolean; // --no-agents-md => false\n  mcp?: boolean; // --no-mcp => false\n  mcpClient?: string[];\n  gitignore?: boolean; // --no-gitignore => false\n  redact?: boolean; // --no-redact => false\n  withHook?: boolean;\n  index?: boolean; // --no-index => false\n  printConfig?: boolean;\n};\n\ntype Answers = {\n  projectName: string;\n  attribution: AttributionEnv;\n  writeEnv: boolean;\n  rcPath: string;\n  redact: boolean;\n  withHook: boolean;\n  writeAgentsMd: boolean;\n  writeGitignore: boolean;\n  mcpClients: McpClient[];\n};\n\n/** Detect the user's shell rc file from $SHELL, defaulting to ~/.zshrc. */\nfunction detectShellRc(): string {\n  const shell = process.env.SHELL ?? '';\n  const home = homedir();\n  if (shell.includes('bash')) return path.join(home, '.bashrc');\n  return path.join(home, '.zshrc');\n}\n\n/** Default project name: package.json \"name\", else the folder basename. */\nfunction defaultProjectName(cwd: string): string {\n  const pkgPath = path.join(cwd, 'package.json');\n  if (existsSync(pkgPath)) {\n    try {\n      const pkg = JSON.parse(readFileSync(pkgPath, 'utf8')) as { name?: string };\n      if (pkg.name && typeof pkg.name === 'string') {\n        return pkg.name.replace(/^@[^/]+\\//, '');\n      }\n    } catch {\n      // ignore malformed package.json\n    }\n  }\n  return path.basename(path.resolve(cwd));\n}\n\n/** Step 0: preflight — git repo check (offer git init), MCP client detection. */\nasync function preflight(cwd: string, flags: InitFlags): Promise<void> {\n  if (!(await isGitRepo(cwd))) {\n    const doInit = await promptConfirm({\n      message: 'This is not a Git repository. Run `git init`?',\n      defaultValue: true,\n    });\n    if (doInit) {\n      const result = await git(cwd, ['init']);\n      if (result !== null) out.ok('Initialized a Git repository.');\n      else out.warn('Could not run `git init`; continuing without Git.');\n    }\n  }\n  void flags;\n}\n\n/** Resolve the set of MCP clients to register, honoring --mcp-client / --no-mcp. */\nasync function resolveMcpClients(cwd: string, flags: InitFlags): Promise<McpClient[]> {\n  if (flags.mcp === false) return [];\n\n  if (flags.mcpClient && flags.mcpClient.length > 0) {\n    const chosen: McpClient[] = [];\n    for (const name of flags.mcpClient) {\n      const client = getMcpClient(name);\n      if (client) chosen.push(client);\n      else out.warn(`Unknown MCP client \"${name}\" — skipping.`);\n    }\n    return chosen;\n  }\n\n  const detected = await detectMcpClients(cwd);\n  if (detected.length === 0) return [];\n\n  return promptMultiselect<McpClient>({\n    message: 'Register the Substrata MCP server with which clients?',\n    choices: detected.map((c) => ({ value: c, label: c.label })),\n    defaultValues: detected,\n  });\n}\n\n/** Collect all wizard answers (no writes). */\nasync function collectAnswers(cwd: string, flags: InitFlags): Promise<Answers> {\n  const projectName =\n    flags.project ??\n    (await promptText({\n      message: 'Project name',\n      defaultValue: defaultProjectName(cwd),\n    }));\n\n  // Agent attribution.\n  const actor = await promptText({\n    message: 'Default actor (agent id)',\n    defaultValue: flags.actor ?? 'unknown-agent',\n  });\n  const model =\n    flags.model ??\n    (await promptText({ message: 'Default agent model (optional)', defaultValue: '' }));\n  const gitEmail = (await git(cwd, ['config', 'user.email'])) ?? '';\n  const requester =\n    flags.requester ??\n    (await promptText({ message: 'Default requester (optional)', defaultValue: gitEmail }));\n\n  const attribution: AttributionEnv = {\n    actor: actor || undefined,\n    model: model || undefined,\n    requester: requester || undefined,\n  };\n\n  const writeEnv =\n    flags.env === false\n      ? false\n      : await promptConfirm({\n          message: 'Persist attribution env vars to your shell rc?',\n          defaultValue: true,\n        });\n\n  const redact =\n    flags.redact === false\n      ? false\n      : await promptConfirm({\n          message: 'Enable security redaction + content scan?',\n          defaultValue: true,\n        });\n\n  const withHook =\n    flags.withHook === true\n      ? true\n      : await promptConfirm({\n          message: 'Install the pre-commit secret hook?',\n          defaultValue: false,\n        });\n\n  const writeAgentsMd =\n    flags.agentsMd === false\n      ? false\n      : await promptConfirm({\n          message: 'Add the Substrata section to AGENTS.md?',\n          defaultValue: true,\n        });\n\n  const writeGitignore = flags.gitignore !== false;\n\n  const mcpClients = await resolveMcpClients(cwd, flags);\n\n  return {\n    projectName,\n    attribution,\n    writeEnv,\n    rcPath: detectShellRc(),\n    redact,\n    withHook,\n    writeAgentsMd,\n    writeGitignore,\n    mcpClients,\n  };\n}\n\n/** Build the full change plan as dry-run ChangeResults (no writes). */\nasync function buildPlan(cwd: string, answers: Answers): Promise<ChangeResult[]> {\n  const changes: ChangeResult[] = [];\n\n  // Scaffold: simulate by checking what initProject would create.\n  // initProject itself is idempotent (skips existing), but it writes; for the\n  // plan we describe the scaffold as a single logical step.\n  changes.push({\n    path: path.join(cwd, '.substrata'),\n    action: existsSync(path.join(cwd, '.substrata', 'config.yml')) ? 'skip' : 'create',\n    description: 'Substrata scaffold (config, README, footprints, memory, templates)',\n  });\n\n  if (answers.writeGitignore) {\n    changes.push(ensureGitignore(cwd, true));\n  }\n\n  if (\n    answers.writeEnv &&\n    (answers.attribution.actor || answers.attribution.model || answers.attribution.requester)\n  ) {\n    changes.push(writeShellEnv(answers.rcPath, answers.attribution, true));\n  }\n\n  if (answers.writeAgentsMd) {\n    changes.push(upsertAgentsMd(cwd, true));\n  }\n\n  if (answers.withHook) {\n    changes.push(installSecretHook(cwd, true));\n  }\n\n  for (const client of answers.mcpClients) {\n    changes.push(await client.register(cwd, SUBSTRATA_MCP_SPEC, true));\n  }\n\n  return changes;\n}\n\n/** Apply the plan for real (idempotent writers). Returns applied changes. */\nasync function applyPlan(cwd: string, answers: Answers): Promise<ChangeResult[]> {\n  const applied: ChangeResult[] = [];\n\n  applied.push(...(await initProject(cwd, { projectName: answers.projectName })));\n\n  if (answers.writeGitignore) {\n    applied.push(ensureGitignore(cwd, false));\n  }\n\n  if (\n    answers.writeEnv &&\n    (answers.attribution.actor || answers.attribution.model || answers.attribution.requester)\n  ) {\n    applied.push(writeShellEnv(answers.rcPath, answers.attribution, false));\n  } else if (!answers.writeEnv) {\n    printEnvSnippet(answers.attribution);\n  }\n\n  if (answers.writeAgentsMd) {\n    applied.push(upsertAgentsMd(cwd, false));\n  }\n\n  if (answers.withHook) {\n    applied.push(installSecretHook(cwd, false));\n  }\n\n  for (const client of answers.mcpClients) {\n    const result = await client.register(cwd, SUBSTRATA_MCP_SPEC, false);\n    applied.push(result);\n    // Windsurf etc. return a skip with a printable snippet in the description.\n    if (result.action === 'skip' && result.description.includes('\\n')) {\n      out.info(`${client.label}: ${result.description}`);\n    }\n  }\n\n  return applied;\n}\n\n/** Print the export snippet when env persistence is declined (plan §8.1 step 2). */\nfunction printEnvSnippet(attribution: AttributionEnv): void {\n  const lines: string[] = [];\n  if (attribution.actor) lines.push(`export SUBSTRATA_ACTOR=\"${attribution.actor}\"`);\n  if (attribution.model) lines.push(`export SUBSTRATA_MODEL=\"${attribution.model}\"`);\n  if (attribution.requester) lines.push(`export SUBSTRATA_REQUESTER=\"${attribution.requester}\"`);\n  if (lines.length === 0) return;\n  out.info('Add these to your shell rc to attribute footprints:');\n  out.plain(lines.map((l) => `  ${l}`).join('\\n'));\n}\n\n/** Render the resolved config.yml without writing (for --print-config). */\nexport function printResolvedConfig(cwd: string, flags: InitFlags): void {\n  const name = flags.project ?? defaultProjectName(cwd);\n  out.plain(renderConfig(name));\n}\n\nexport type WizardResult = {\n  applied: ChangeResult[];\n  aborted: boolean;\n};\n\n/** Run the full init wizard. Returns whether the user aborted. */\nexport async function runInitWizard(cwd: string, flags: InitFlags): Promise<WizardResult> {\n  const updateMode = existsSync(path.join(cwd, '.substrata', 'config.yml'));\n  if (updateMode) {\n    out.info('Existing .substrata detected — running in update mode.');\n  }\n\n  await preflight(cwd, flags);\n  const answers = await collectAnswers(cwd, flags);\n\n  const plan = await buildPlan(cwd, answers);\n  out.plain(pc.bold('\\nPlanned changes:'));\n  out.plain(\n    plan\n      .map((c) => {\n        const label =\n          c.action === 'create'\n            ? pc.green('CREATE')\n            : c.action === 'update'\n              ? pc.yellow('UPDATE')\n              : pc.dim('SKIP  ');\n        return `  ${label}  ${c.path}${c.description ? pc.dim(` — ${c.description.split('\\n')[0]}`) : ''}`;\n      })\n      .join('\\n'),\n  );\n  out.plain('');\n\n  const confirmed = await promptConfirm({ message: 'Apply these changes?', defaultValue: true });\n  if (!confirmed) {\n    out.info('Aborted. Nothing was written.');\n    return { applied: [], aborted: true };\n  }\n\n  const applied = await applyPlan(cwd, answers);\n  out.ok('Substrata setup applied.');\n\n  if (answers.writeEnv) {\n    out.info(`Run \\`source ${answers.rcPath}\\` to load attribution env vars.`);\n  }\n\n  return { applied, aborted: false };\n}\n","import { execFile } from 'node:child_process';\nimport { existsSync } from 'node:fs';\nimport path from 'node:path';\nimport { promisify } from 'node:util';\n\nimport type { ChangeResult } from '@substrata/core';\n\nimport { mergeMcpJson, removeMcpJson } from './json-config';\nimport type { McpClient, McpServerSpec } from './registry';\n\n/**\n * Claude Code MCP client. Detected via the `claude` binary on PATH OR an existing\n * project `.mcp.json`. Registration writes `.mcp.json` directly (rather than\n * shelling to `claude mcp add`) so it is deterministic and testable.\n */\n\nconst execFileAsync = promisify(execFile);\n\nfunction mcpJsonPath(cwd: string): string {\n  return path.join(cwd, '.mcp.json');\n}\n\nasync function hasClaudeBinary(): Promise<boolean> {\n  try {\n    await execFileAsync('which', ['claude']);\n    return true;\n  } catch {\n    return false;\n  }\n}\n\nexport const claudeCodeClient: McpClient = {\n  name: 'claude',\n  label: 'Claude Code',\n\n  async detect(cwd: string): Promise<boolean> {\n    if (existsSync(mcpJsonPath(cwd))) return true;\n    return hasClaudeBinary();\n  },\n\n  async register(cwd: string, spec: McpServerSpec, dry: boolean = false): Promise<ChangeResult> {\n    return mergeMcpJson(mcpJsonPath(cwd), spec, dry);\n  },\n\n  async unregister(cwd: string, name: string): Promise<void> {\n    removeMcpJson(mcpJsonPath(cwd), name);\n  },\n};\n","import { lstatSync, readFileSync, writeFileSync, mkdirSync } from 'node:fs';\nimport path from 'node:path';\n\nimport type { ChangeResult } from '@substrata/core';\n\nimport type { McpServerSpec } from './registry';\n\n/**\n * Shared helper for clients that store MCP servers in a JSON file under an\n * `mcpServers` map (Claude Code `.mcp.json`, Cursor `.cursor/mcp.json`). The\n * write is idempotent: remove-then-add the named entry, preserving other keys.\n */\n\ntype McpJson = {\n  mcpServers?: Record<string, { command: string; args?: string[] }>;\n  [key: string]: unknown;\n};\n\nfunction isSymlink(filePath: string): boolean {\n  try {\n    return lstatSync(filePath).isSymbolicLink();\n  } catch {\n    return false;\n  }\n}\n\nfunction readJson(filePath: string): McpJson | null {\n  try {\n    const raw = readFileSync(filePath, 'utf8');\n    const parsed = JSON.parse(raw) as unknown;\n    return parsed && typeof parsed === 'object' ? (parsed as McpJson) : {};\n  } catch {\n    return null;\n  }\n}\n\n/** Whether the existing config already contains the spec entry exactly. */\nfunction entryMatches(existing: McpJson | null, spec: McpServerSpec): boolean {\n  const entry = existing?.mcpServers?.[spec.name];\n  if (!entry) return false;\n  return (\n    entry.command === spec.command && JSON.stringify(entry.args ?? []) === JSON.stringify(spec.args)\n  );\n}\n\n/**\n * Merge the Substrata MCP server into a JSON config file at `filePath`.\n * Remove-then-add semantics keep the result idempotent across reruns.\n */\nexport function mergeMcpJson(\n  filePath: string,\n  spec: McpServerSpec,\n  dry: boolean = false,\n): ChangeResult {\n  // Refuse to write through a symlink: a repo-shipped link could redirect the\n  // merge into a file outside the repo.\n  if (isSymlink(filePath)) {\n    return {\n      path: filePath,\n      action: 'skip',\n      description: `refused: ${path.basename(filePath)} is a symlink`,\n    };\n  }\n  const existing = readJson(filePath);\n\n  if (entryMatches(existing, spec)) {\n    return { path: filePath, action: 'skip', description: 'MCP entry already current' };\n  }\n\n  const base: McpJson = existing ?? {};\n  const servers = { ...(base.mcpServers ?? {}) };\n  // Remove-then-add so a drifted entry is replaced wholesale.\n  delete servers[spec.name];\n  servers[spec.name] = { command: spec.command, args: spec.args };\n\n  const next: McpJson = { ...base, mcpServers: servers };\n  const contents = `${JSON.stringify(next, null, 2)}\\n`;\n\n  if (!dry) {\n    mkdirSync(path.dirname(filePath), { recursive: true });\n    writeFileSync(filePath, contents, 'utf8');\n  }\n\n  return {\n    path: filePath,\n    action: existing === null ? 'create' : 'update',\n    description: `register Substrata MCP server (${spec.name})`,\n    contents,\n  };\n}\n\n/** Remove the named MCP entry from a JSON config file (idempotent). */\nexport function removeMcpJson(filePath: string, name: string): void {\n  const existing = readJson(filePath);\n  if (!existing?.mcpServers?.[name]) return;\n  const servers = { ...existing.mcpServers };\n  delete servers[name];\n  const next: McpJson = { ...existing, mcpServers: servers };\n  writeFileSync(filePath, `${JSON.stringify(next, null, 2)}\\n`, 'utf8');\n}\n","import { existsSync } from 'node:fs';\nimport path from 'node:path';\n\nimport type { ChangeResult } from '@substrata/core';\n\nimport { mergeMcpJson, removeMcpJson } from './json-config';\nimport type { McpClient, McpServerSpec } from './registry';\n\n/**\n * Cursor MCP client. Stores project MCP servers in `.cursor/mcp.json` using the\n * same `mcpServers` map shape as Claude Code. Detected via an existing\n * `.cursor/` directory or `.cursor/mcp.json`.\n */\n\nfunction cursorMcpPath(cwd: string): string {\n  return path.join(cwd, '.cursor', 'mcp.json');\n}\n\nexport const cursorClient: McpClient = {\n  name: 'cursor',\n  label: 'Cursor',\n\n  async detect(cwd: string): Promise<boolean> {\n    return existsSync(path.join(cwd, '.cursor')) || existsSync(cursorMcpPath(cwd));\n  },\n\n  async register(cwd: string, spec: McpServerSpec, dry: boolean = false): Promise<ChangeResult> {\n    return mergeMcpJson(cursorMcpPath(cwd), spec, dry);\n  },\n\n  async unregister(cwd: string, name: string): Promise<void> {\n    removeMcpJson(cursorMcpPath(cwd), name);\n  },\n};\n","import { existsSync } from 'node:fs';\nimport { homedir } from 'node:os';\nimport path from 'node:path';\n\nimport type { ChangeResult } from '@substrata/core';\n\nimport type { McpClient, McpServerSpec } from './registry';\n\n/**\n * Windsurf MCP client. Windsurf's MCP config is global per-user\n * (`~/.codeium/windsurf/mcp_config.json`), so registration does NOT edit the\n * user's homedir. Instead it returns a `skip` ChangeResult whose description is a\n * printable snippet + path the user can apply manually.\n */\n\nfunction windsurfConfigPath(): string {\n  return path.join(homedir(), '.codeium', 'windsurf', 'mcp_config.json');\n}\n\nfunction snippet(spec: McpServerSpec): string {\n  const block = {\n    mcpServers: {\n      [spec.name]: { command: spec.command, args: spec.args },\n    },\n  };\n  return `${windsurfConfigPath()}\\n${JSON.stringify(block, null, 2)}`;\n}\n\nexport const windsurfClient: McpClient = {\n  name: 'windsurf',\n  label: 'Windsurf',\n\n  async detect(): Promise<boolean> {\n    return existsSync(path.join(homedir(), '.codeium', 'windsurf'));\n  },\n\n  async register(_cwd: string, spec: McpServerSpec): Promise<ChangeResult> {\n    // Global config — never write into the user's homedir; print a snippet.\n    return {\n      path: windsurfConfigPath(),\n      action: 'skip',\n      description: `add manually (global config):\\n${snippet(spec)}`,\n    };\n  },\n\n  async unregister(): Promise<void> {\n    // No-op: Windsurf config is user-global and not managed by Substrata.\n  },\n};\n","import type { ChangeResult } from '@substrata/core';\n\nimport { claudeCodeClient } from './claude-code';\nimport { cursorClient } from './cursor';\nimport { windsurfClient } from './windsurf';\n\n/**\n * MCP client registry (plan §14). A small table so new clients can be added\n * without touching the wizard flow. Each client can detect whether it is present,\n * register the Substrata MCP server (idempotent, dry-runnable), and unregister.\n */\n\n/** Spec for the Substrata MCP server entry written into client config. */\nexport type McpServerSpec = {\n  /** Logical name of the server entry (the key in the client's config map). */\n  name: string;\n  command: string;\n  args: string[];\n};\n\nexport type McpClient = {\n  /** Stable id: \"claude\" | \"cursor\" | \"windsurf\". */\n  name: string;\n  /** Human-friendly label for prompts. */\n  label: string;\n  detect(cwd: string): Promise<boolean>;\n  register(cwd: string, spec: McpServerSpec, dry?: boolean): Promise<ChangeResult>;\n  unregister(cwd: string, name: string): Promise<void>;\n};\n\n/** The default Substrata MCP server spec written into client configs. */\nexport const SUBSTRATA_MCP_SPEC: McpServerSpec = {\n  name: 'substrata',\n  command: 'npx',\n  args: ['-y', 'substrata-cli', 'mcp'],\n};\n\nexport const MCP_CLIENTS: McpClient[] = [claudeCodeClient, cursorClient, windsurfClient];\n\n/** Look up a client by its stable id. */\nexport function getMcpClient(name: string): McpClient | undefined {\n  return MCP_CLIENTS.find((c) => c.name === name);\n}\n\n/** Detect which registered clients are present in/around `cwd`. */\nexport async function detectMcpClients(cwd: string): Promise<McpClient[]> {\n  const detected: McpClient[] = [];\n  for (const client of MCP_CLIENTS) {\n    if (await client.detect(cwd)) detected.push(client);\n  }\n  return detected;\n}\n","import type { SearchResult } from '@substrata/core';\nimport pc from 'picocolors';\n\n/**\n * Human-readable rendering of search results and footprint lists. Output is\n * informative, not noisy: one block per result with id, title, status, tags,\n * path, and a snippet.\n */\n\nfunction statusLabel(status: SearchResult['status']): string {\n  switch (status) {\n    case 'superseded':\n      return pc.yellow('[superseded]');\n    case 'deprecated':\n      return pc.red('[deprecated]');\n    case 'draft':\n      return pc.dim('[draft]');\n    default:\n      return '';\n  }\n}\n\n/** Render a list of search results for the terminal. */\nexport function renderSearchResults(results: SearchResult[]): string {\n  if (results.length === 0) {\n    return pc.dim('No matching footprints or memory found.');\n  }\n  const blocks = results.map((r, i) => {\n    const n = pc.dim(`${i + 1}.`);\n    const status = statusLabel(r.status);\n    const header = `${n} ${pc.bold(r.title || r.id)}${status ? ` ${status}` : ''}`;\n    const lines = [header, `   ${pc.dim('id:')} ${r.id}`, `   ${pc.dim('path:')} ${r.filePath}`];\n    if (r.tags.length > 0) lines.push(`   ${pc.dim('tags:')} ${r.tags.join(', ')}`);\n    if (r.snippet.trim().length > 0) {\n      lines.push(`   ${pc.dim(r.snippet.replace(/\\s+/g, ' ').trim())}`);\n    }\n    return lines.join('\\n');\n  });\n  return blocks.join('\\n\\n');\n}\n\n/** Render footprints (from `list`) as compact rows. */\nexport function renderFootprintList(\n  rows: Array<{\n    id: string;\n    title: string;\n    status: SearchResult['status'];\n    createdAt?: string;\n    tags: string[];\n  }>,\n): string {\n  if (rows.length === 0) {\n    return pc.dim('No footprints found.');\n  }\n  return rows\n    .map((r) => {\n      const date = r.createdAt ? r.createdAt.slice(0, 10) : '----------';\n      const status = statusLabel(r.status);\n      const tags = r.tags.length > 0 ? pc.dim(` (${r.tags.join(', ')})`) : '';\n      return `${pc.dim(date)}  ${pc.bold(r.title || r.id)}${status ? ` ${status}` : ''}\\n  ${pc.dim(r.id)}${tags}`;\n    })\n    .join('\\n');\n}\n","import { listFootprints, type Footprint } from '@substrata/core';\nimport type { Command } from 'commander';\n\nimport { renderFootprintList } from '../render/table';\nimport { out, requireConfig, resolveCwd } from '../util';\n\n/**\n * `substrata list` — list footprints filtered by tag/file/since. No index needed;\n * reads footprint files directly (plan §8.6).\n */\n\ntype ListOptions = {\n  tag?: string;\n  file?: string;\n  since?: string;\n  json?: boolean;\n};\n\nfunction matches(fp: Footprint, opts: ListOptions): boolean {\n  if (opts.tag && !(fp.frontmatter.tags ?? []).includes(opts.tag)) return false;\n  if (opts.file && !(fp.frontmatter.files_touched ?? []).includes(opts.file)) return false;\n  if (opts.since && fp.frontmatter.created_at < opts.since) return false;\n  return true;\n}\n\nexport function registerListCommand(program: Command): void {\n  program\n    .command('list')\n    .description('List recent footprints')\n    .option('--tag <tag>', 'Only footprints carrying this tag')\n    .option('--file <path>', 'Only footprints touching this file')\n    .option('--since <date>', 'Only footprints created on/after this ISO date')\n    .option('--json', 'Output JSON')\n    .action(async (opts: ListOptions, command: Command) => {\n      const cwd = resolveCwd(command.parent?.opts());\n      await requireConfig(cwd);\n\n      const all = await listFootprints(cwd);\n      const filtered = all.filter((fp) => matches(fp, opts));\n\n      if (opts.json) {\n        const rows = filtered.map((fp) => ({\n          id: fp.frontmatter.id,\n          title: fp.title,\n          status: fp.frontmatter.status,\n          createdAt: fp.frontmatter.created_at,\n          tags: fp.frontmatter.tags ?? [],\n          filesTouched: fp.frontmatter.files_touched ?? [],\n          filePath: fp.filePath,\n        }));\n        out.plain(JSON.stringify(rows, null, 2));\n        return;\n      }\n\n      out.plain(\n        renderFootprintList(\n          filtered.map((fp) => ({\n            id: fp.frontmatter.id,\n            title: fp.title,\n            status: fp.frontmatter.status,\n            createdAt: fp.frontmatter.created_at,\n            tags: fp.frontmatter.tags ?? [],\n          })),\n        ),\n      );\n    });\n}\n","import type { Command } from 'commander';\n\nimport { CliError, resolveCwd } from '../util';\n\n/**\n * `substrata mcp` — run the MCP server (plan §8.12). Dynamically imports\n * `@substrata/mcp-server` (built in parallel) and calls its documented contract:\n *   runMcpServer(options?: { cwd?: string }): Promise<void>\n */\n\ntype McpServerModule = {\n  runMcpServer: (options?: { cwd?: string }) => Promise<void>;\n};\n\nexport function registerMcpCommand(program: Command): void {\n  program\n    .command('mcp')\n    .description('Run the Substrata MCP server (stdio)')\n    .action(async (_opts: unknown, command: Command) => {\n      const cwd = resolveCwd(command.parent?.opts());\n      let mod: McpServerModule;\n      try {\n        mod = (await import('@substrata/mcp-server')) as unknown as McpServerModule;\n      } catch (err) {\n        throw new CliError(`Failed to load @substrata/mcp-server: ${(err as Error).message}`);\n      }\n      if (typeof mod.runMcpServer !== 'function') {\n        throw new CliError('@substrata/mcp-server does not export runMcpServer().');\n      }\n      await mod.runMcpServer({ cwd });\n    });\n}\n","import { existsSync } from 'node:fs';\nimport { readFile, writeFile } from 'node:fs/promises';\nimport path from 'node:path';\n\nimport {\n  appendMemoryEntries,\n  existingEntryIds,\n  listFootprints,\n  memoryDir,\n  type MemoryEntry,\n} from '@substrata/core';\nimport type { Command } from 'commander';\n\nimport { promptConfirm, isNonInteractive } from '../wizard/prompts';\nimport { out, requireConfig, resolveCwd } from '../util';\n\n/**\n * `substrata memory update` — scan footprints, extract `Memory learned` sections,\n * suggest entries, confirm, and append them before the entries:end marker of\n * `.substrata/memory/conventions.md` (created with frontmatter if missing).\n * Idempotent: entries whose source footprint id already appears are skipped\n * (plan §8.10).\n */\n\nconst CONVENTIONS_FRONTMATTER = `---\nschema_version: 1\nid: mem_repo_conventions\ntype: repo_conventions\ntags:\n  - conventions\n---\n\n# Repo conventions\n\nCurated, durable knowledge agents should read often.\n\n<!-- substrata:entries:start -->\n<!-- substrata:entries:end -->\n`;\n\ntype MemoryUpdateOptions = {\n  since?: string;\n  yes?: boolean;\n};\n\nexport function registerMemoryUpdateCommand(program: Command): void {\n  const memory = program.command('memory').description('Curated memory utilities');\n\n  memory\n    .command('update')\n    .description('Suggest and append memory entries from footprints')\n    .option('--since <date>', 'Only footprints created on/after this ISO date')\n    .option('--yes', 'Append without confirmation')\n    .action(async (opts: MemoryUpdateOptions, command: Command) => {\n      // `memory` is the parent of `update`; the program is its grandparent.\n      const cwd = resolveCwd(command.parent?.parent?.opts());\n      await requireConfig(cwd);\n\n      const footprints = await listFootprints(cwd);\n      const filtered = opts.since\n        ? footprints.filter((fp) => fp.frontmatter.created_at >= opts.since!)\n        : footprints;\n\n      const candidates: MemoryEntry[] = [];\n      for (const fp of filtered) {\n        const learned = fp.sections.memoryLearned ?? [];\n        if (learned.length === 0) continue;\n        candidates.push({\n          sourceId: fp.frontmatter.id,\n          lines: learned.map((l) => `- ${l}`),\n        });\n      }\n\n      if (candidates.length === 0) {\n        out.info('No `Memory learned` sections found in the selected footprints.');\n        return;\n      }\n\n      const filePath = path.join(memoryDir(cwd), 'conventions.md');\n\n      // Compute which entries are genuinely new (idempotent preview).\n      const alreadyPresent = existsSync(filePath)\n        ? existingEntryIds(await readFile(filePath, 'utf8'))\n        : new Set<string>();\n      const fresh = candidates.filter((c) => !alreadyPresent.has(c.sourceId));\n\n      if (fresh.length === 0) {\n        out.info('All suggested entries are already present. Nothing to do.');\n        return;\n      }\n\n      out.plain('Suggested memory entries:');\n      for (const entry of fresh) {\n        out.plain(`  [${entry.sourceId}]`);\n        for (const line of entry.lines) out.plain(`    ${line}`);\n      }\n\n      const confirmed =\n        opts.yes || isNonInteractive()\n          ? true\n          : await promptConfirm({\n              message: `Append ${fresh.length} entr${fresh.length === 1 ? 'y' : 'ies'} to conventions.md?`,\n              defaultValue: true,\n            });\n\n      if (!confirmed) {\n        out.info('Aborted. Nothing written.');\n        return;\n      }\n\n      if (!existsSync(filePath)) {\n        await writeFile(filePath, CONVENTIONS_FRONTMATTER, 'utf8');\n      }\n\n      const changed = await appendMemoryEntries(filePath, candidates);\n      if (changed) {\n        out.ok(`Appended ${fresh.length} memory entr${fresh.length === 1 ? 'y' : 'ies'}.`);\n      } else {\n        out.info('No new entries appended (already present).');\n      }\n    });\n}\n","import { search } from '@substrata/search';\nimport type { Command } from 'commander';\n\nimport { renderSearchResults } from '../render/table';\nimport { out, requireConfig, resolveCwd } from '../util';\n\nimport { ensureFreshIndex } from './auto-index';\n\n/**\n * `substrata search <query>` — full-text search over footprints + memory.\n * Auto-(re)builds a stale/missing index unless `--no-auto-index`. By default\n * includes superseded footprints (demoted in ranking) so humans can trace\n * history; `--exclude-superseded` drops them (plan §8.3).\n */\n\ntype SearchOptions = {\n  json?: boolean;\n  files?: string[];\n  tag?: string[];\n  limit?: string;\n  excludeSuperseded?: boolean;\n  autoIndex?: boolean;\n};\n\nfunction collect(value: string, previous: string[] = []): string[] {\n  return [...previous, value];\n}\n\nexport function registerSearchCommand(program: Command): void {\n  program\n    .command('search <query>')\n    .description('Search footprints and memory')\n    .option('--json', 'Output JSON')\n    .option('--files <path>', 'Filter to docs touching this file (repeatable)', collect, [])\n    .option('--tag <tag>', 'Filter to docs carrying this tag (repeatable)', collect, [])\n    .option('--limit <n>', 'Maximum number of results')\n    .option('--exclude-superseded', 'Drop superseded/deprecated footprints')\n    .option('--no-auto-index', 'Do not auto-(re)build a stale/missing index')\n    .action(async (query: string, opts: SearchOptions, command: Command) => {\n      const cwd = resolveCwd(command.parent?.opts());\n      const config = await requireConfig(cwd);\n\n      await ensureFreshIndex(cwd, opts.autoIndex !== false);\n\n      const limit = opts.limit ? Number(opts.limit) : config.search.default_limit;\n      const results = await search(query, {\n        cwd,\n        limit: Number.isFinite(limit) ? limit : config.search.default_limit,\n        files: opts.files && opts.files.length > 0 ? opts.files : undefined,\n        tags: opts.tag && opts.tag.length > 0 ? opts.tag : undefined,\n        excludeSuperseded: opts.excludeSuperseded,\n      });\n\n      if (opts.json) {\n        out.plain(JSON.stringify(results, null, 2));\n        return;\n      }\n      out.plain(renderSearchResults(results));\n    });\n}\n","import { findFootprintById } from '@substrata/core';\nimport type { Command } from 'commander';\nimport pc from 'picocolors';\n\nimport { CliError, out, requireConfig, resolveCwd } from '../util';\n\n/**\n * `substrata show <id>` — pretty-print one footprint, or its JSON / path.\n * (plan §8.7)\n */\n\ntype ShowOptions = {\n  json?: boolean;\n  path?: boolean;\n};\n\nexport function registerShowCommand(program: Command): void {\n  program\n    .command('show <id>')\n    .description('Show one footprint')\n    .option('--json', 'Output the parsed footprint as JSON')\n    .option('--path', 'Print only the footprint file path')\n    .action(async (id: string, opts: ShowOptions, command: Command) => {\n      const cwd = resolveCwd(command.parent?.opts());\n      await requireConfig(cwd);\n\n      const fp = await findFootprintById(cwd, id);\n      if (!fp) throw new CliError(`Footprint not found: ${id}`);\n\n      if (opts.path) {\n        out.plain(fp.filePath);\n        return;\n      }\n\n      if (opts.json) {\n        out.plain(\n          JSON.stringify(\n            {\n              id: fp.frontmatter.id,\n              title: fp.title,\n              filePath: fp.filePath,\n              frontmatter: fp.frontmatter,\n              sections: fp.sections,\n            },\n            null,\n            2,\n          ),\n        );\n        return;\n      }\n\n      const fm = fp.frontmatter;\n      const lines: string[] = [\n        pc.bold(fp.title || fm.id),\n        `${pc.dim('id:')}        ${fm.id}`,\n        `${pc.dim('status:')}    ${fm.status}`,\n        `${pc.dim('work_type:')} ${fm.work_type}`,\n        `${pc.dim('actor:')}     ${fm.actor}`,\n      ];\n      if (fm.requester) lines.push(`${pc.dim('requester:')} ${fm.requester}`);\n      if (fm.agent_model) lines.push(`${pc.dim('model:')}     ${fm.agent_model}`);\n      lines.push(`${pc.dim('created:')}   ${fm.created_at}`);\n      if (fm.tags && fm.tags.length > 0)\n        lines.push(`${pc.dim('tags:')}      ${fm.tags.join(', ')}`);\n      if (fm.files_touched && fm.files_touched.length > 0) {\n        lines.push(`${pc.dim('files:')}     ${fm.files_touched.join(', ')}`);\n      }\n      lines.push(`${pc.dim('path:')}      ${fp.filePath}`);\n      lines.push('');\n      lines.push(fp.body.trim());\n      out.plain(lines.join('\\n'));\n    });\n}\n","import { NotFoundError, supersedeFootprint } from '@substrata/core';\nimport { buildIndex } from '@substrata/search';\nimport type { Command } from 'commander';\n\nimport { CliError, out, requireConfig, resolveCwd } from '../util';\n\n/**\n * `substrata supersede <old-id> --by <new-id>` — mark an old footprint replaced\n * by a new one (frontmatter-only edits), then rebuild the index so ranking\n * reflects the new status (plan §8.9).\n */\nexport function registerSupersedeCommand(program: Command): void {\n  program\n    .command('supersede <old-id>')\n    .description('Mark an old footprint as superseded by a new one')\n    .requiredOption('--by <new-id>', 'Id of the footprint that replaces the old one')\n    .action(async (oldId: string, opts: { by: string }, command: Command) => {\n      const cwd = resolveCwd(command.parent?.opts());\n      await requireConfig(cwd);\n\n      try {\n        await supersedeFootprint(cwd, oldId, opts.by);\n      } catch (err) {\n        if (err instanceof NotFoundError) throw new CliError(err.message);\n        throw err;\n      }\n\n      await buildIndex(cwd);\n      out.ok(`${oldId} superseded by ${opts.by}. Index rebuilt.`);\n    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