substrata-cli 0.1.0 → 0.1.1

package/dist/chunk-5V44C5UO.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../../core/src/errors.ts","../../core/src/paths.ts","../../core/src/ids.ts","../../core/src/markdown.ts","../../core/src/config.ts","../../core/src/redaction.ts","../../core/src/footprint.ts","../../core/src/memory.ts","../../core/src/supersede.ts","../../core/src/init.ts","../../core/src/setup/gitignore.ts","../../core/src/setup/symlink.ts","../../core/src/setup/shellrc.ts","../../core/src/setup/agents-md.ts","../../core/src/setup/hook.ts","../../core/src/setup/plan.ts","../../search/src/indexer.ts","../../search/src/schema.ts","../../search/src/sqlite.ts","../../search/src/freshness.ts","../../search/src/query.ts","../../search/src/ranking.ts"],"sourcesContent":["import type { SecretFinding } from './types';\n\n/** Base error for all Substrata failures. */\nexport class SubstrataError extends Error {\n  constructor(message: string) {\n    super(message);\n    this.name = 'SubstrataError';\n  }\n}\n\n/** Configuration is missing, malformed, or has an unsupported schema_version. */\nexport class ConfigError extends SubstrataError {\n  constructor(message: string) {\n    super(message);\n    this.name = 'ConfigError';\n  }\n}\n\n/** A footprint/memory file could not be parsed or is missing required metadata. */\nexport class ParseError extends SubstrataError {\n  readonly filePath?: string;\n\n  constructor(message: string, filePath?: string) {\n    super(filePath ? `${message} (${filePath})` : message);\n    this.name = 'ParseError';\n    this.filePath = filePath;\n  }\n}\n\n/** One or more secrets were detected and the write was refused. */\nexport class SecretDetectedError extends SubstrataError {\n  readonly findings: SecretFinding[];\n\n  constructor(findings: SecretFinding[]) {\n    const detail = findings.map((f) => `${f.name} at line ${f.line}`).join(', ');\n    super(`Refusing to write: ${findings.length} potential secret(s) detected: ${detail}`);\n    this.name = 'SecretDetectedError';\n    this.findings = findings;\n  }\n}\n\n/** A requested resource (e.g. a footprint id) could not be found. */\nexport class NotFoundError extends SubstrataError {\n  constructor(message: string) {\n    super(message);\n    this.name = 'NotFoundError';\n  }\n}\n","import path from 'node:path';\n\n/**\n * Path helpers for the .substrata directory.\n *\n * Repo-relative paths are always emitted with forward slashes so footprint\n * `file_path` values and config storage paths are stable across platforms.\n * Absolute on-disk paths use the platform separator (via node:path).\n */\n\nexport const SUBSTRATA_DIRNAME = '.substrata';\n\n/** Convert any path to forward-slash form. */\nexport function toPosix(p: string): string {\n  return p.split(path.sep).join('/');\n}\n\n/** Absolute path to the .substrata directory. */\nexport function substrataDir(cwd: string): string {\n  return path.join(cwd, SUBSTRATA_DIRNAME);\n}\n\n/** Absolute path to config.yml. */\nexport function configPath(cwd: string): string {\n  return path.join(substrataDir(cwd), 'config.yml');\n}\n\n/** Absolute path to the footprints directory. */\nexport function footprintsDir(cwd: string): string {\n  return path.join(substrataDir(cwd), 'footprints');\n}\n\n/** Absolute path to the memory directory. */\nexport function memoryDir(cwd: string): string {\n  return path.join(substrataDir(cwd), 'memory');\n}\n\n/** Absolute path to the templates directory. */\nexport function templatesDir(cwd: string): string {\n  return path.join(substrataDir(cwd), 'templates');\n}\n\n/** Absolute path to the generated SQLite index. */\nexport function indexPath(cwd: string): string {\n  return path.join(substrataDir(cwd), 'index', 'footprint.sqlite');\n}\n\n/**\n * Repo-relative footprint path of the form\n * `YYYY/MM/YYYY-MM-DD-<slug>-<suffix>.md` (forward slashes).\n */\nexport function footprintRelativePath(date: Date, slug: string, suffix: string): string {\n  const yyyy = String(date.getUTCFullYear()).padStart(4, '0');\n  const mm = String(date.getUTCMonth() + 1).padStart(2, '0');\n  const dd = String(date.getUTCDate()).padStart(2, '0');\n  const filename = `${yyyy}-${mm}-${dd}-${slug}-${suffix}.md`;\n  return `${yyyy}/${mm}/${filename}`;\n}\n\n/** Absolute on-disk path for a footprint, given its repo-relative path. */\nexport function footprintFilePath(cwd: string, relativePath: string): string {\n  return path.join(footprintsDir(cwd), ...relativePath.split('/'));\n}\n\n/** Repo-relative (forward-slash) path from an absolute path. */\nexport function relativeToCwd(cwd: string, absolutePath: string): string {\n  return toPosix(path.relative(cwd, absolutePath));\n}\n","import { randomBytes } from 'node:crypto';\n\n/**\n * ID and filename generation for footprints. See plan §5.\n *\n *   id        : fp_<YYYYMMDD>_<slug_underscored>_<suffix>\n *   filename  : YYYY/MM/YYYY-MM-DD-<slug>-<suffix>.md\n */\n\n/** Crockford-ish base32 alphabet without confusing chars (no i/l/o/u). */\nconst SUFFIX_ALPHABET = 'abcdefghjkmnpqrstvwxyz0123456789';\nconst SUFFIX_LENGTH = 6;\n\n/**\n * Slugify a title into a lowercase, hyphenated slug suitable for filenames.\n * Non-alphanumeric runs become single hyphens; leading/trailing hyphens trimmed.\n */\nexport function slugify(title: string): string {\n  const slug = title\n    .normalize('NFKD')\n    // strip combining diacritical marks\n    .replace(/[̀-ͯ]/g, '')\n    .toLowerCase()\n    .replace(/[^a-z0-9]+/g, '-')\n    .replace(/^-+|-+$/g, '');\n  return slug || 'untitled';\n}\n\n/** Generate a random lowercase base32 suffix (default 6 chars). */\nexport function randomSuffix(length: number = SUFFIX_LENGTH): string {\n  const bytes = randomBytes(length);\n  let out = '';\n  for (let i = 0; i < length; i++) {\n    out += SUFFIX_ALPHABET[bytes[i]! % SUFFIX_ALPHABET.length];\n  }\n  return out;\n}\n\n/**\n * Build a footprint id from a date and slug.\n * The slug is underscored (hyphens → underscores) per the id format.\n */\nexport function generateFootprintId(date: Date, slug: string, suffix?: string): string {\n  const yyyy = String(date.getUTCFullYear()).padStart(4, '0');\n  const mm = String(date.getUTCMonth() + 1).padStart(2, '0');\n  const dd = String(date.getUTCDate()).padStart(2, '0');\n  const underscored = slug.replace(/-/g, '_');\n  const sfx = suffix ?? randomSuffix();\n  return `fp_${yyyy}${mm}${dd}_${underscored}_${sfx}`;\n}\n\n/** Build the repo-relative footprint filename `YYYY/MM/YYYY-MM-DD-<slug>-<suffix>.md`. */\nexport function buildFootprintFilename(date: Date, slug: string, suffix: string): string {\n  const yyyy = String(date.getUTCFullYear()).padStart(4, '0');\n  const mm = String(date.getUTCMonth() + 1).padStart(2, '0');\n  const dd = String(date.getUTCDate()).padStart(2, '0');\n  return `${yyyy}/${mm}/${yyyy}-${mm}-${dd}-${slug}-${suffix}.md`;\n}\n","import { parse as parseYaml, stringify as stringifyYaml } from 'yaml';\n\nimport type { FootprintSections, RejectedOption } from './types';\n\n/**\n * Frontmatter + section rendering/parsing for footprint markdown bodies.\n *\n * Frontmatter uses the `yaml` package. Body sections follow the layout in\n * plan §5 (Purpose, Decisions, Rejected options, Implementation notes,\n * Commands run, Memory learned, Future agent guidance).\n */\n\nconst FRONTMATTER_RE = /^---\\r?\\n([\\s\\S]*?)\\r?\\n---\\r?\\n?([\\s\\S]*)$/;\n\nexport type ParsedFrontmatter = {\n  /** Parsed YAML frontmatter object (empty object when none present). */\n  frontmatter: Record<string, unknown>;\n  /** Body text after the closing `---`. */\n  body: string;\n};\n\n/** Split a raw markdown document into frontmatter + body. */\nexport function parseFrontmatter(raw: string): ParsedFrontmatter {\n  const match = FRONTMATTER_RE.exec(raw);\n  if (!match) {\n    return { frontmatter: {}, body: raw };\n  }\n  const parsed = parseYaml(match[1]!) as unknown;\n  const frontmatter =\n    parsed && typeof parsed === 'object' ? (parsed as Record<string, unknown>) : {};\n  return { frontmatter, body: match[2] ?? '' };\n}\n\n/** Serialize a frontmatter object and body back into a markdown document. */\nexport function serializeFrontmatter(frontmatter: Record<string, unknown>, body: string): string {\n  const yaml = stringifyYaml(frontmatter, { lineWidth: 0 }).trimEnd();\n  const trimmedBody = body.replace(/^\\r?\\n+/, '');\n  return `---\\n${yaml}\\n---\\n\\n${trimmedBody.length > 0 ? `${trimmedBody.replace(/\\s+$/, '')}\\n` : ''}`;\n}\n\n/** Title is the first level-1 heading; returns '' if absent. */\nexport function extractTitle(body: string): string {\n  const match = /^#\\s+(.+?)\\s*$/m.exec(body);\n  return match ? match[1]!.trim() : '';\n}\n\n// --- Section rendering -------------------------------------------------------\n\nfunction renderListSection(heading: string, items: string[] | undefined): string | null {\n  if (!items || items.length === 0) return null;\n  const lines = items.map((item) => `- ${item}`);\n  return `## ${heading}\\n\\n${lines.join('\\n')}`;\n}\n\nfunction renderProseSection(heading: string, text: string | undefined): string | null {\n  if (!text || text.trim().length === 0) return null;\n  return `## ${heading}\\n\\n${text.trim()}`;\n}\n\nfunction renderRejectedOptions(options: RejectedOption[] | undefined): string | null {\n  if (!options || options.length === 0) return null;\n  const blocks = options.map((o) => `### ${o.option}\\n\\n${o.reason.trim()}`);\n  return `## Rejected options\\n\\n${blocks.join('\\n\\n')}`;\n}\n\nfunction renderCommands(commands: string[] | undefined): string | null {\n  if (!commands || commands.length === 0) return null;\n  return `## Commands run\\n\\n\\`\\`\\`bash\\n${commands.join('\\n')}\\n\\`\\`\\``;\n}\n\n/**\n * Render the full footprint body from a title and structured sections.\n * Only non-empty sections are emitted, in canonical order.\n */\nexport function renderFootprintBody(title: string, sections: FootprintSections): string {\n  const parts: Array<string | null> = [\n    `# ${title}`,\n    renderProseSection('Purpose', sections.purpose),\n    renderListSection('Decisions', sections.decisions),\n    renderRejectedOptions(sections.rejectedOptions),\n    renderProseSection('Implementation notes', sections.implementationNotes),\n    renderCommands(sections.commandsRun),\n    renderListSection('Memory learned', sections.memoryLearned),\n    renderProseSection('Future agent guidance', sections.futureAgentGuidance),\n  ];\n  return `${parts.filter((p): p is string => p !== null).join('\\n\\n')}\\n`;\n}\n\n// --- Section parsing ---------------------------------------------------------\n\ntype RawSection = { heading: string; content: string };\n\n/** Split a body into level-2 (`##`) sections, ignoring the title and preamble. */\nfunction splitSections(body: string): RawSection[] {\n  const lines = body.split(/\\r?\\n/);\n  const sections: RawSection[] = [];\n  let current: RawSection | null = null;\n  let inFence = false;\n\n  for (const line of lines) {\n    if (/^```/.test(line.trim())) {\n      inFence = !inFence;\n      if (current) current.content += `${line}\\n`;\n      continue;\n    }\n    const headingMatch = !inFence ? /^##\\s+(.+?)\\s*$/.exec(line) : null;\n    if (headingMatch) {\n      if (current) sections.push(current);\n      current = { heading: headingMatch[1]!.trim(), content: '' };\n      continue;\n    }\n    if (current) current.content += `${line}\\n`;\n  }\n  if (current) sections.push(current);\n  return sections;\n}\n\nfunction parseListItems(content: string): string[] {\n  return content\n    .split(/\\r?\\n/)\n    .map((l) => l.trim())\n    .filter((l) => l.startsWith('- '))\n    .map((l) => l.slice(2).trim())\n    .filter((l) => l.length > 0);\n}\n\nfunction parseProse(content: string): string {\n  return content.trim();\n}\n\nfunction parseCommands(content: string): string[] {\n  const fenceMatch = /```(?:bash|sh)?\\r?\\n([\\s\\S]*?)```/.exec(content);\n  const inner = fenceMatch ? fenceMatch[1]! : content;\n  return inner\n    .split(/\\r?\\n/)\n    .map((l) => l.trim())\n    .filter((l) => l.length > 0);\n}\n\nfunction parseRejectedOptions(content: string): RejectedOption[] {\n  const options: RejectedOption[] = [];\n  const parts = content.split(/^###\\s+/m);\n  for (const part of parts) {\n    const trimmed = part.trim();\n    if (!trimmed) continue;\n    const newlineIdx = trimmed.indexOf('\\n');\n    if (newlineIdx === -1) {\n      options.push({ option: trimmed, reason: '' });\n      continue;\n    }\n    const option = trimmed.slice(0, newlineIdx).trim();\n    const reason = trimmed.slice(newlineIdx + 1).trim();\n    options.push({ option, reason });\n  }\n  return options;\n}\n\n/** Parse a footprint body into structured sections. Headings are case-insensitive. */\nexport function parseFootprintBody(body: string): FootprintSections {\n  const sections: FootprintSections = {};\n  for (const raw of splitSections(body)) {\n    const key = raw.heading.toLowerCase();\n    switch (key) {\n      case 'purpose':\n        sections.purpose = parseProse(raw.content);\n        break;\n      case 'decisions':\n        sections.decisions = parseListItems(raw.content);\n        break;\n      case 'rejected options':\n        sections.rejectedOptions = parseRejectedOptions(raw.content);\n        break;\n      case 'implementation notes':\n        sections.implementationNotes = parseProse(raw.content);\n        break;\n      case 'commands run':\n        sections.commandsRun = parseCommands(raw.content);\n        break;\n      case 'memory learned':\n        sections.memoryLearned = parseListItems(raw.content);\n        break;\n      case 'future agent guidance':\n        sections.futureAgentGuidance = parseProse(raw.content);\n        break;\n      default:\n        break;\n    }\n  }\n  return sections;\n}\n","import { readFile } from 'node:fs/promises';\nimport path from 'node:path';\n\nimport { parse as parseYaml, stringify as stringifyYaml } from 'yaml';\n\nimport { ConfigError } from './errors';\nimport { configPath } from './paths';\nimport type { SubstrataConfig } from './types';\n\n/**\n * Default redaction keys (plan §12). The redactor also matches kebab/snake\n * variants case-insensitively, so only the canonical forms are listed.\n */\nexport const DEFAULT_REDACTION_KEYS: string[] = [\n  'token',\n  'apiKey',\n  'api_key',\n  'authorization',\n  'password',\n  'secret',\n  'cookie',\n  'set-cookie',\n  'privateKey',\n  'accessToken',\n  'refreshToken',\n];\n\n/** Default config shape (plan §13). projectName is filled by loadConfig/init. */\nexport const defaultConfig: SubstrataConfig = {\n  schema_version: 1,\n  project: {\n    name: 'substrata-demo',\n  },\n  storage: {\n    footprints_dir: '.substrata/footprints',\n    memory_dir: '.substrata/memory',\n    index_path: '.substrata/index/footprint.sqlite',\n  },\n  search: {\n    default_limit: 8,\n    max_context_tokens: 1600,\n  },\n  security: {\n    redact: true,\n    scan_content: true,\n    entropy_scan: false,\n    entropy_min_length: 32,\n    block_on_secret: true,\n    redaction_keys: [\n      'token',\n      'apiKey',\n      'api_key',\n      'authorization',\n      'password',\n      'secret',\n      'cookie',\n      'privateKey',\n      'accessToken',\n      'refreshToken',\n    ],\n  },\n  agent: {\n    default_actor: 'unknown-agent',\n    require_footprint_after_non_trivial_work: true,\n  },\n};\n\nfunction isObject(value: unknown): value is Record<string, unknown> {\n  return typeof value === 'object' && value !== null && !Array.isArray(value);\n}\n\n/** Deep-merge `override` onto `base`. Arrays and scalars from override win wholesale. */\nfunction deepMerge<T>(base: T, override: unknown): T {\n  if (!isObject(base) || !isObject(override)) {\n    return override === undefined ? base : (override as T);\n  }\n  const result: Record<string, unknown> = { ...base };\n  for (const [key, value] of Object.entries(override)) {\n    if (value === undefined) continue;\n    const baseValue = (base as Record<string, unknown>)[key];\n    if (isObject(baseValue) && isObject(value)) {\n      result[key] = deepMerge(baseValue, value);\n    } else {\n      result[key] = value;\n    }\n  }\n  return result as T;\n}\n\n/**\n * Load `.substrata/config.yml`, deep-merging user values over defaults.\n * Throws ConfigError if the file is missing/malformed or schema_version !== 1.\n * The default project name falls back to the cwd basename.\n */\nexport async function loadConfig(cwd: string): Promise<SubstrataConfig> {\n  const file = configPath(cwd);\n  let raw: string;\n  try {\n    raw = await readFile(file, 'utf8');\n  } catch {\n    throw new ConfigError(`Config not found at ${file}. Run \\`substrata init\\`.`);\n  }\n\n  let parsed: unknown;\n  try {\n    parsed = parseYaml(raw);\n  } catch (err) {\n    throw new ConfigError(`Failed to parse ${file}: ${(err as Error).message}`);\n  }\n\n  if (!isObject(parsed)) {\n    throw new ConfigError(`Config at ${file} must be a YAML mapping.`);\n  }\n\n  if (parsed.schema_version !== 1) {\n    throw new ConfigError(\n      `Unsupported config schema_version: ${String(parsed.schema_version)} (expected 1).`,\n    );\n  }\n\n  const base: SubstrataConfig = {\n    ...defaultConfig,\n    project: { name: path.basename(cwd) },\n  };\n  return deepMerge(base, parsed);\n}\n\n/** Render a config.yml file for `init`, overriding the project name. */\nexport function renderConfig(projectName: string): string {\n  const config: SubstrataConfig = {\n    ...defaultConfig,\n    project: { name: projectName },\n  };\n  return stringifyYaml(config, { lineWidth: 0 });\n}\n","import type { RedactionOptions, SecretFinding } from './types';\n\n/**\n * Redaction (key-based) + content/pattern secret scanning. See plan §12.\n */\n\nexport const DEFAULT_REDACTION_KEYS: string[] = [\n  'token',\n  'apiKey',\n  'api_key',\n  'authorization',\n  'password',\n  'secret',\n  'cookie',\n  'set-cookie',\n  'privateKey',\n  'accessToken',\n  'refreshToken',\n];\n\nconst REDACTED = '[REDACTED]';\n\n/** Normalize a key for matching: lowercase, strip `-`/`_` separators. */\nfunction normalizeKey(key: string): string {\n  return key.toLowerCase().replace(/[-_]/g, '');\n}\n\n/**\n * Recursively replace values whose key matches a redaction key (case-insensitive,\n * ignoring kebab/snake separators) with `[REDACTED]`. Returns a new structure;\n * the input is not mutated.\n */\nexport function redactDeep(value: unknown, options: RedactionOptions = {}): unknown {\n  const keys = options.keys ?? DEFAULT_REDACTION_KEYS;\n  const replacement = options.replacement ?? REDACTED;\n  const normalizedKeys = new Set(keys.map(normalizeKey));\n\n  const walk = (node: unknown): unknown => {\n    if (Array.isArray(node)) {\n      return node.map(walk);\n    }\n    if (node && typeof node === 'object') {\n      const out: Record<string, unknown> = {};\n      for (const [k, v] of Object.entries(node as Record<string, unknown>)) {\n        if (normalizedKeys.has(normalizeKey(k))) {\n          out[k] = replacement;\n        } else {\n          out[k] = walk(v);\n        }\n      }\n      return out;\n    }\n    return node;\n  };\n\n  return walk(value);\n}\n\n/** Content secret patterns (plan §12). */\nexport const SECRET_PATTERNS: Array<{ name: string; re: RegExp }> = [\n  { name: 'aws_access_key_id', re: /\\bAKIA[0-9A-Z]{16}\\b/ },\n  { name: 'github_pat', re: /\\bghp_[A-Za-z0-9]{36}\\b/ },\n  { name: 'github_fine_grained', re: /\\bgithub_pat_[A-Za-z0-9_]{60,}\\b/ },\n  { name: 'gitlab_pat', re: /\\bglpat-[A-Za-z0-9_-]{20}\\b/ },\n  { name: 'slack_token', re: /\\bxox[baprs]-[A-Za-z0-9-]{10,}\\b/ },\n  { name: 'google_api_key', re: /\\bAIza[0-9A-Za-z_-]{35}\\b/ },\n  { name: 'openai_key', re: /\\bsk-[A-Za-z0-9]{20,}\\b/ },\n  { name: 'anthropic_key', re: /\\bsk-ant-[A-Za-z0-9_-]{20,}\\b/ },\n  {\n    name: 'jwt',\n    re: /\\beyJ[A-Za-z0-9_-]{10,}\\.[A-Za-z0-9_-]{10,}\\.[A-Za-z0-9_-]{10,}\\b/,\n  },\n  {\n    name: 'private_key_block',\n    re: /-----BEGIN (?:RSA |EC |OPENSSH |DSA |PGP )?PRIVATE KEY-----/,\n  },\n  { name: 'bearer_header', re: /\\bBearer\\s+[A-Za-z0-9._-]{20,}\\b/ },\n  { name: 'url_basic_auth', re: /\\b[a-z][a-z0-9+.-]*:\\/\\/[^/\\s:@]+:[^/\\s:@]+@/i },\n];\n\n/**\n * Scan text for secrets, returning findings with 1-based line numbers.\n * Each pattern may match multiple times across lines.\n */\nexport function scanForSecrets(text: string): SecretFinding[] {\n  const findings: SecretFinding[] = [];\n  const lines = text.split(/\\r?\\n/);\n  for (let i = 0; i < lines.length; i++) {\n    const line = lines[i]!;\n    for (const { name, re } of SECRET_PATTERNS) {\n      // Use a fresh non-global regex test per line to avoid lastIndex state.\n      if (re.test(line)) {\n        findings.push({ name, line: i + 1 });\n      }\n    }\n  }\n  return findings;\n}\n\n/**\n * Replace secret-pattern matches in text with `[REDACTED:<name>]`.\n * Returns the redacted text; does not detect entropy-based secrets.\n */\nexport function redactText(text: string): string {\n  let out = text;\n  for (const { name, re } of SECRET_PATTERNS) {\n    const globalRe = new RegExp(re.source, re.flags.includes('g') ? re.flags : `${re.flags}g`);\n    out = out.replace(globalRe, `[REDACTED:${name}]`);\n  }\n  return out;\n}\n\n/**\n * Optional high-entropy heuristic, off by default. Flags long standalone tokens\n * whose Shannon entropy exceeds a threshold. Gated by `options.enabled`.\n */\nexport function scanForHighEntropy(\n  text: string,\n  options: { enabled?: boolean; minLength?: number; minEntropy?: number } = {},\n): SecretFinding[] {\n  if (!options.enabled) return [];\n  const minLength = options.minLength ?? 32;\n  const minEntropy = options.minEntropy ?? 4.0;\n  const findings: SecretFinding[] = [];\n  const lines = text.split(/\\r?\\n/);\n  for (let i = 0; i < lines.length; i++) {\n    const tokens = lines[i]!.split(/[\\s\"'`(),;]+/);\n    for (const token of tokens) {\n      if (token.length >= minLength && shannonEntropy(token) >= minEntropy) {\n        findings.push({ name: 'high_entropy', line: i + 1 });\n        break;\n      }\n    }\n  }\n  return findings;\n}\n\nfunction shannonEntropy(s: string): number {\n  const counts = new Map<string, number>();\n  for (const ch of s) counts.set(ch, (counts.get(ch) ?? 0) + 1);\n  let entropy = 0;\n  for (const count of counts.values()) {\n    const p = count / s.length;\n    entropy -= p * Math.log2(p);\n  }\n  return entropy;\n}\n","import type { Dirent } from 'node:fs';\nimport { mkdir, readdir, readFile, writeFile } from 'node:fs/promises';\nimport path from 'node:path';\n\nimport { loadConfig } from './config';\nimport { ParseError, SecretDetectedError } from './errors';\nimport { buildFootprintFilename, generateFootprintId, randomSuffix, slugify } from './ids';\nimport {\n  extractTitle,\n  parseFootprintBody,\n  parseFrontmatter,\n  renderFootprintBody,\n  serializeFrontmatter,\n} from './markdown';\nimport { footprintsDir, relativeToCwd } from './paths';\nimport { redactDeep, scanForSecrets } from './redaction';\nimport type {\n  Footprint,\n  FootprintFrontmatter,\n  FootprintRelated,\n  FootprintStatus,\n  SecretFinding,\n  WorkType,\n  WriteFootprintInput,\n} from './types';\n\nconst REQUIRED_KEYS = [\n  'schema_version',\n  'id',\n  'created_at',\n  'actor',\n  'work_type',\n  'status',\n] as const;\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\nconst VALID_STATUSES: ReadonlySet<string> = new Set<FootprintStatus>([\n  'draft',\n  'completed',\n  'superseded',\n  'deprecated',\n]);\n\nfunction validateFrontmatter(fm: Record<string, unknown>, filePath?: string): FootprintFrontmatter {\n  for (const key of REQUIRED_KEYS) {\n    if (fm[key] === undefined || fm[key] === null) {\n      throw new ParseError(`Footprint missing required frontmatter field \"${key}\"`, filePath);\n    }\n  }\n  if (fm.schema_version !== 1) {\n    throw new ParseError(\n      `Footprint has unsupported schema_version: ${String(fm.schema_version)} (expected 1)`,\n      filePath,\n    );\n  }\n  if (typeof fm.id !== 'string' || fm.id.length === 0) {\n    throw new ParseError('Footprint \"id\" must be a non-empty string', filePath);\n  }\n  if (typeof fm.actor !== 'string' || fm.actor.length === 0) {\n    throw new ParseError('Footprint \"actor\" must be a non-empty string', filePath);\n  }\n  if (typeof fm.created_at !== 'string' || fm.created_at.length === 0) {\n    throw new ParseError('Footprint \"created_at\" must be a non-empty string', filePath);\n  }\n  if (typeof fm.work_type !== 'string' || !VALID_WORK_TYPES.has(fm.work_type)) {\n    throw new ParseError(`Footprint has invalid work_type: ${String(fm.work_type)}`, filePath);\n  }\n  if (typeof fm.status !== 'string' || !VALID_STATUSES.has(fm.status)) {\n    throw new ParseError(`Footprint has invalid status: ${String(fm.status)}`, filePath);\n  }\n  return fm as FootprintFrontmatter;\n}\n\n/** Parse raw markdown into a Footprint, validating required frontmatter. */\nexport function parseFootprint(raw: string, filePath: string): Footprint {\n  const { frontmatter, body } = parseFrontmatter(raw);\n  const fm = validateFrontmatter(frontmatter, filePath);\n  const title = extractTitle(body);\n  const sections = parseFootprintBody(body);\n  return { frontmatter: fm, title, body, sections, filePath, raw };\n}\n\n/** Read and parse a footprint file from disk. */\nexport async function parseFootprintFile(filePath: string): Promise<Footprint> {\n  let raw: string;\n  try {\n    raw = await readFile(filePath, 'utf8');\n  } catch {\n    throw new ParseError('Footprint file could not be read', filePath);\n  }\n  return parseFootprint(raw, filePath);\n}\n\nfunction mergeSupersedes(\n  related: FootprintRelated | undefined,\n  supersedes: string[] | undefined,\n): FootprintRelated | undefined {\n  if (!related && (!supersedes || supersedes.length === 0)) return undefined;\n  const merged: FootprintRelated = { ...(related ?? {}) };\n  if (supersedes && supersedes.length > 0) {\n    const existing = merged.supersedes ?? [];\n    merged.supersedes = Array.from(new Set([...existing, ...supersedes]));\n  }\n  return merged;\n}\n\n/** Drop undefined/empty fields so YAML frontmatter stays clean. */\nfunction cleanFrontmatter(fm: FootprintFrontmatter): Record<string, unknown> {\n  const out: Record<string, unknown> = {\n    schema_version: fm.schema_version,\n    id: fm.id,\n    created_at: fm.created_at,\n  };\n  if (fm.updated_at) out.updated_at = fm.updated_at;\n  out.actor = fm.actor;\n  if (fm.requester) out.requester = fm.requester;\n  if (fm.agent_model) out.agent_model = fm.agent_model;\n  out.work_type = fm.work_type;\n  out.status = fm.status;\n  if (fm.repo && (fm.repo.name || fm.repo.branch)) out.repo = fm.repo;\n  if (fm.related && Object.keys(fm.related).length > 0) out.related = fm.related;\n  if (fm.files_touched && fm.files_touched.length > 0) out.files_touched = fm.files_touched;\n  if (fm.tags && fm.tags.length > 0) out.tags = fm.tags;\n  return out;\n}\n\n/**\n * `files_touched` entries land in committed frontmatter and are matched against\n * repo paths by search — only plain repo-relative paths are meaningful, and\n * absolute or `..`-traversing entries are likely mistakes (or mischief).\n */\nfunction validateFilesTouched(files: string[] | undefined): string[] | undefined {\n  if (!files || files.length === 0) return undefined;\n  return files.map((entry) => {\n    // Normalize separators explicitly (not via toPosix): entries are plain\n    // strings that may carry Windows separators regardless of host platform.\n    const f = entry.trim().replace(/\\\\/g, '/');\n    if (f === '') {\n      throw new ParseError('files_touched entries must be non-empty repo-relative paths');\n    }\n    if (f.startsWith('/') || /^[A-Za-z]:\\//.test(f)) {\n      throw new ParseError(`files_touched must be repo-relative, got absolute path: ${f}`);\n    }\n    if (f.split('/').includes('..')) {\n      throw new ParseError(`files_touched must not contain '..' segments: ${f}`);\n    }\n    return f;\n  });\n}\n\nfunction validateRelatedUrls(related: FootprintRelated | undefined): void {\n  for (const u of related?.urls ?? []) {\n    let parsed: URL;\n    try {\n      parsed = new URL(u);\n    } catch {\n      throw new ParseError(`related.urls entry is not a valid URL: ${u}`);\n    }\n    if (parsed.protocol !== 'http:' && parsed.protocol !== 'https:') {\n      throw new ParseError(`related.urls only allows http(s) URLs, got: ${u}`);\n    }\n  }\n}\n\n/**\n * Write a new footprint: resolve config, generate id/filename, render markdown,\n * run redaction + secret scan, write the file, and return the parsed Footprint.\n * Throws SecretDetectedError when secrets remain and block_on_secret is set\n * (unless `allowSecret` is true).\n */\nexport async function writeFootprint(\n  input: WriteFootprintInput & { cwd: string },\n): Promise<Footprint> {\n  const { cwd } = input;\n  const config = await loadConfig(cwd);\n\n  const createdAt = input.createdAt ?? new Date().toISOString();\n  const date = new Date(createdAt);\n  const slug = slugify(input.title);\n  const suffix = randomSuffix();\n  const id = generateFootprintId(date, slug, suffix);\n  const relPath = buildFootprintFilename(date, slug, suffix);\n  const absPath = path.join(footprintsDir(cwd), ...relPath.split('/'));\n\n  const workType: WorkType = input.workType ?? 'implementation';\n  const status: FootprintStatus = input.status ?? 'completed';\n\n  const filesTouched = validateFilesTouched(input.filesTouched);\n\n  // Key-based redaction (plan §12) applies to structured frontmatter values\n  // (e.g. nested objects under repo/related). It does not touch prose.\n  const related = mergeSupersedes(input.related, input.supersedes);\n  validateRelatedUrls(related);\n  const frontmatter: FootprintFrontmatter = {\n    schema_version: 1,\n    id,\n    created_at: createdAt,\n    actor: input.actor,\n    requester: input.requester,\n    agent_model: input.agentModel,\n    work_type: workType,\n    status,\n    repo: input.repo\n      ? (redactDeep(input.repo, { keys: config.security.redaction_keys }) as typeof input.repo)\n      : undefined,\n    related: related\n      ? (redactDeep(related, { keys: config.security.redaction_keys }) as typeof related)\n      : undefined,\n    files_touched: filesTouched,\n    tags: input.tags,\n  };\n\n  // Render the body from structured sections.\n  const body = renderFootprintBody(input.title, {\n    purpose: input.purpose,\n    decisions: input.decisions,\n    rejectedOptions: input.rejectedOptions,\n    implementationNotes: input.implementationNotes,\n    commandsRun: input.commandsRun,\n    memoryLearned: input.memoryLearned,\n    futureAgentGuidance: input.futureAgentGuidance,\n  });\n\n  // Content (pattern) scan over the rendered body. Key-based redaction does not\n  // mask prose secrets, so any remaining match blocks the write (plan §12).\n  if (config.security.scan_content) {\n    const findings: SecretFinding[] = scanForSecrets(body);\n    if (findings.length > 0 && config.security.block_on_secret && !input.allowSecret) {\n      throw new SecretDetectedError(findings);\n    }\n  }\n\n  const raw = serializeFrontmatter(cleanFrontmatter(frontmatter), body);\n\n  await mkdir(path.dirname(absPath), { recursive: true });\n  await writeFile(absPath, raw, 'utf8');\n\n  return parseFootprint(raw, absPath);\n}\n\nasync function walkMarkdown(dir: string): Promise<string[]> {\n  let entries: Dirent[];\n  try {\n    entries = await readdir(dir, { withFileTypes: true });\n  } catch {\n    return [];\n  }\n  const files: string[] = [];\n  for (const entry of entries) {\n    const full = path.join(dir, entry.name);\n    if (entry.isDirectory()) {\n      files.push(...(await walkMarkdown(full)));\n    } else if (entry.isFile() && entry.name.endsWith('.md')) {\n      files.push(full);\n    }\n  }\n  return files;\n}\n\n/** List all footprints under the footprints dir, sorted by created_at desc. */\nexport async function listFootprints(cwd: string): Promise<Footprint[]> {\n  const dir = footprintsDir(cwd);\n  const files = await walkMarkdown(dir);\n  const footprints = await Promise.all(files.map((f) => parseFootprintFile(f)));\n  footprints.sort((a, b) => {\n    const at = a.frontmatter.created_at;\n    const bt = b.frontmatter.created_at;\n    return at < bt ? 1 : at > bt ? -1 : 0;\n  });\n  return footprints;\n}\n\n/** Find a footprint by id; returns null if not present. */\nexport async function findFootprintById(cwd: string, id: string): Promise<Footprint | null> {\n  const files = await walkMarkdown(footprintsDir(cwd));\n  for (const file of files) {\n    const fp = await parseFootprintFile(file);\n    if (fp.frontmatter.id === id) return fp;\n  }\n  return null;\n}\n\n/** Compute the repo-relative (forward-slash) path of a footprint. */\nexport function footprintRepoPath(cwd: string, fp: Footprint): string {\n  return relativeToCwd(cwd, fp.filePath);\n}\n","import type { Dirent } from 'node:fs';\nimport { readdir, readFile, writeFile } from 'node:fs/promises';\nimport path from 'node:path';\n\nimport { ParseError } from './errors';\nimport { extractTitle, parseFrontmatter } from './markdown';\nimport { memoryDir } from './paths';\nimport type { MemoryDocument, MemoryFrontmatter } from './types';\n\n/**\n * Curated memory parsing + append-friendly entry insertion. See plan §6.\n *\n * Entries live between stable markers:\n *   <!-- substrata:entries:start -->\n *   ... entries ...\n *   <!-- substrata:entries:end -->\n *\n * Each entry is wrapped in:\n *   <!-- substrata:entry id=<sourceId> -->\n *   <lines>\n *   <!-- /substrata:entry -->\n */\n\nconst ENTRIES_START = '<!-- substrata:entries:start -->';\nconst ENTRIES_END = '<!-- substrata:entries:end -->';\n\nfunction entryOpen(id: string): string {\n  return `<!-- substrata:entry id=${id} -->`;\n}\nconst ENTRY_CLOSE = '<!-- /substrata:entry -->';\n\nfunction validateMemoryFrontmatter(\n  fm: Record<string, unknown>,\n  filePath: string,\n): MemoryFrontmatter {\n  if (fm.schema_version !== 1) {\n    throw new ParseError(\n      `Memory file has unsupported schema_version: ${String(fm.schema_version)} (expected 1)`,\n      filePath,\n    );\n  }\n  if (typeof fm.id !== 'string' || fm.id.length === 0) {\n    throw new ParseError('Memory \"id\" must be a non-empty string', filePath);\n  }\n  return fm as MemoryFrontmatter;\n}\n\n/** Parse raw markdown into a MemoryDocument. */\nexport function parseMemory(raw: string, filePath: string): MemoryDocument {\n  const { frontmatter, body } = parseFrontmatter(raw);\n  const fm = validateMemoryFrontmatter(frontmatter, filePath);\n  return { frontmatter: fm, title: extractTitle(body), body, filePath, raw };\n}\n\n/** Read and parse a memory file from disk. */\nexport async function parseMemoryFile(filePath: string): Promise<MemoryDocument> {\n  let raw: string;\n  try {\n    raw = await readFile(filePath, 'utf8');\n  } catch {\n    throw new ParseError('Memory file could not be read', filePath);\n  }\n  return parseMemory(raw, filePath);\n}\n\nasync function walkMarkdown(dir: string): Promise<string[]> {\n  let entries: Dirent[];\n  try {\n    entries = await readdir(dir, { withFileTypes: true });\n  } catch {\n    return [];\n  }\n  const files: string[] = [];\n  for (const entry of entries) {\n    const full = path.join(dir, entry.name);\n    if (entry.isDirectory()) {\n      files.push(...(await walkMarkdown(full)));\n    } else if (entry.isFile() && entry.name.endsWith('.md')) {\n      files.push(full);\n    }\n  }\n  return files;\n}\n\n/** List all memory documents under the memory dir, sorted by file path. */\nexport async function listMemoryDocuments(cwd: string): Promise<MemoryDocument[]> {\n  const files = await walkMarkdown(memoryDir(cwd));\n  files.sort();\n  return Promise.all(files.map((f) => parseMemoryFile(f)));\n}\n\nexport type MemoryEntry = {\n  sourceId: string;\n  lines: string[];\n};\n\n/** Extract the set of sourceIds already present in a memory file body. */\nexport function existingEntryIds(content: string): Set<string> {\n  const ids = new Set<string>();\n  const re = /<!--\\s*substrata:entry\\s+id=([^\\s]+)\\s*-->/g;\n  let match: RegExpExecArray | null;\n  while ((match = re.exec(content)) !== null) {\n    ids.add(match[1]!);\n  }\n  return ids;\n}\n\nfunction renderEntry(entry: MemoryEntry): string {\n  return [entryOpen(entry.sourceId), ...entry.lines, ENTRY_CLOSE].join('\\n');\n}\n\n/**\n * Append entries to a memory file before the entries:end marker, creating the\n * marker block if absent. Existing content is preserved byte-for-byte; entries\n * whose sourceId already appears in the file are skipped (idempotent).\n * Returns true if the file was changed.\n */\nexport async function appendMemoryEntries(\n  filePath: string,\n  entries: MemoryEntry[],\n): Promise<boolean> {\n  const original = await readFile(filePath, 'utf8');\n  const existing = existingEntryIds(original);\n  const toAdd = entries.filter((e) => !existing.has(e.sourceId));\n  if (toAdd.length === 0) return false;\n\n  const rendered = toAdd.map(renderEntry).join('\\n');\n\n  let next: string;\n  const endIdx = original.indexOf(ENTRIES_END);\n  if (endIdx !== -1) {\n    // Insert before the existing end marker, preserving everything around it.\n    const before = original.slice(0, endIdx);\n    const after = original.slice(endIdx);\n    const sep = before.endsWith('\\n') ? '' : '\\n';\n    next = `${before}${sep}${rendered}\\n${after}`;\n  } else {\n    // No marker block: create one at the end of the file.\n    const base = original.endsWith('\\n') ? original : `${original}\\n`;\n    next = `${base}\\n${ENTRIES_START}\\n${rendered}\\n${ENTRIES_END}\\n`;\n  }\n\n  await writeFile(filePath, next, 'utf8');\n  return true;\n}\n","import { readFile, writeFile } from 'node:fs/promises';\n\nimport { parse as parseYaml, stringify as stringifyYaml } from 'yaml';\n\nimport { NotFoundError } from './errors';\nimport { findFootprintById } from './footprint';\nimport type { FootprintRelated } from './types';\n\n/**\n * Supersede relationship editing. See plan §5/§8.9.\n *\n * Edits ONLY the YAML frontmatter of both files (old + new); the markdown body\n * is preserved byte-for-byte. Old footprint gets status=superseded and\n * superseded_by += newId; new footprint gets supersedes += oldId.\n */\n\nconst FRONTMATTER_RE = /^(---\\r?\\n)([\\s\\S]*?)(\\r?\\n---\\r?\\n?)([\\s\\S]*)$/;\n\nfunction addUnique(list: string[] | undefined, value: string): string[] {\n  const arr = list ? [...list] : [];\n  if (!arr.includes(value)) arr.push(value);\n  return arr;\n}\n\n/**\n * Rewrite a footprint file's frontmatter via `mutate`, preserving the exact\n * body bytes and the original frontmatter fences/newlines.\n */\nasync function editFrontmatter(\n  filePath: string,\n  mutate: (fm: Record<string, unknown>) => void,\n): Promise<void> {\n  const raw = await readFile(filePath, 'utf8');\n  const match = FRONTMATTER_RE.exec(raw);\n  if (!match) {\n    throw new NotFoundError(`Footprint at ${filePath} has no parseable frontmatter`);\n  }\n  const [, open, yamlText, close, body] = match;\n  const parsed = parseYaml(yamlText!) as Record<string, unknown>;\n  mutate(parsed);\n  const newYaml = stringifyYaml(parsed, { lineWidth: 0 }).replace(/\\n$/, '');\n  const next = `${open}${newYaml}${close}${body}`;\n  await writeFile(filePath, next, 'utf8');\n}\n\n/**\n * Mark `oldId` as superseded by `newId`. Edits frontmatter only on both files.\n * Throws NotFoundError if either id cannot be located.\n */\nexport async function supersedeFootprint(cwd: string, oldId: string, newId: string): Promise<void> {\n  const oldFp = await findFootprintById(cwd, oldId);\n  if (!oldFp) throw new NotFoundError(`Footprint not found: ${oldId}`);\n  const newFp = await findFootprintById(cwd, newId);\n  if (!newFp) throw new NotFoundError(`Footprint not found: ${newId}`);\n\n  await editFrontmatter(oldFp.filePath, (fm) => {\n    fm.status = 'superseded';\n    const related = (fm.related as FootprintRelated | undefined) ?? {};\n    related.superseded_by = addUnique(related.superseded_by, newId);\n    fm.related = related;\n  });\n\n  await editFrontmatter(newFp.filePath, (fm) => {\n    const related = (fm.related as FootprintRelated | undefined) ?? {};\n    related.supersedes = addUnique(related.supersedes, oldId);\n    fm.related = related;\n  });\n}\n","import { mkdir, writeFile } from 'node:fs/promises';\nimport path from 'node:path';\n\nimport { renderConfig } from './config';\nimport { configPath, footprintsDir, memoryDir, substrataDir, templatesDir } from './paths';\nimport type { ChangeResult, InitOptions } from './types';\n\n/**\n * Project scaffolding for `substrata init`. Idempotent: existing files are never\n * overwritten. See plan §8.1 (\"Created on apply\") and §14.\n */\n\nconst README_CONTENTS = `# Substrata\n\nThis directory holds shared agent memory for this repository.\n\n- \\`footprints/\\` — committed source-of-truth records of agent-assisted work.\n- \\`memory/\\` — curated, durable repo knowledge agents should read often.\n- \\`templates/\\` — templates used when creating footprints and memory files.\n- \\`config.yml\\` — Substrata configuration (see the docs).\n- \\`index/\\` and \\`cache/\\` — generated, gitignored; safe to delete and rebuild.\n\nFootprints and memory files are committed. Do not store secrets, credentials,\nprivate keys, tokens, or sensitive user data here.\n`;\n\nconst FOOTPRINT_TEMPLATE = `---\nschema_version: 1\nid: fp_YYYYMMDD_slug_suffix\ncreated_at: 2026-01-01T00:00:00Z\nactor: unknown-agent\nwork_type: implementation\nstatus: completed\n---\n\n# Title\n\n## Purpose\n\nWhy this work was done.\n\n## Decisions\n\n- Decision one.\n\n## Rejected options\n\n### Option name\n\nWhy it was rejected.\n\n## Implementation notes\n\nWhat was changed.\n\n## Commands run\n\n\\`\\`\\`bash\npnpm test\n\\`\\`\\`\n\n## Memory learned\n\n- Something durable about this repo.\n\n## Future agent guidance\n\nWhat a future agent should check before changing this area.\n`;\n\nconst MEMORY_TEMPLATE = `---\nschema_version: 1\nid: mem_example\ntype: repo_conventions\ntags:\n  - conventions\n---\n\n# Memory title\n\n## Section\n\n- Durable note one.\n\n<!-- substrata:entries:start -->\n<!-- substrata:entries:end -->\n`;\n\ntype FileSpec = { absPath: string; contents: string };\ntype DirSpec = string;\n\nasync function exists(p: string): Promise<boolean> {\n  const { stat } = await import('node:fs/promises');\n  try {\n    await stat(p);\n    return true;\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Create the .substrata scaffold. Never overwrites existing files/dirs.\n * Returns the list of changes applied (create/skip per path).\n */\nexport async function initProject(cwd: string, options: InitOptions = {}): Promise<ChangeResult[]> {\n  const projectName = options.projectName ?? path.basename(path.resolve(cwd));\n\n  const dirs: DirSpec[] = [\n    substrataDir(cwd),\n    footprintsDir(cwd),\n    memoryDir(cwd),\n    templatesDir(cwd),\n  ];\n\n  const files: FileSpec[] = [\n    { absPath: configPath(cwd), contents: renderConfig(projectName) },\n    { absPath: path.join(substrataDir(cwd), 'README.md'), contents: README_CONTENTS },\n    { absPath: path.join(templatesDir(cwd), 'footprint.md'), contents: FOOTPRINT_TEMPLATE },\n    { absPath: path.join(templatesDir(cwd), 'memory.md'), contents: MEMORY_TEMPLATE },\n  ];\n\n  const changes: ChangeResult[] = [];\n\n  for (const dir of dirs) {\n    await mkdir(dir, { recursive: true });\n  }\n\n  for (const file of files) {\n    if (await exists(file.absPath)) {\n      changes.push({\n        path: file.absPath,\n        action: 'skip',\n        description: 'already exists',\n      });\n      continue;\n    }\n    await writeFile(file.absPath, file.contents, 'utf8');\n    changes.push({\n      path: file.absPath,\n      action: 'create',\n      description: 'created',\n      contents: file.contents,\n    });\n  }\n\n  return changes;\n}\n","import { readFileSync, writeFileSync } from 'node:fs';\nimport path from 'node:path';\n\nimport type { ChangeResult } from '../types';\nimport { isSymlink } from './symlink';\n\n/**\n * Ensure `.gitignore` ignores Substrata's generated directories without\n * duplicating lines. Pure + dry-runnable.\n */\n\nexport const GITIGNORE_LINES = ['.substrata/index/', '.substrata/cache/', '.substrata/tmp/'];\n\nfunction readIfExists(filePath: string): string | null {\n  try {\n    return readFileSync(filePath, 'utf8');\n  } catch {\n    return null;\n  }\n}\n\nexport function ensureGitignore(cwd: string, dry: boolean = false): ChangeResult {\n  const filePath = path.join(cwd, '.gitignore');\n  if (isSymlink(filePath)) {\n    return { path: filePath, action: 'skip', description: 'refused: .gitignore is a symlink' };\n  }\n  const existing = readIfExists(filePath);\n  const present = existing ?? '';\n  const presentLines = new Set(present.split(/\\r?\\n/).map((l) => l.trim()));\n\n  const missing = GITIGNORE_LINES.filter((line) => !presentLines.has(line));\n\n  if (missing.length === 0) {\n    return {\n      path: filePath,\n      action: 'skip',\n      description: existing === null ? 'no gitignore needed' : 'gitignore already covers Substrata',\n    };\n  }\n\n  const header = '# Substrata generated files';\n  const block = presentLines.has(header) ? missing.join('\\n') : `${header}\\n${missing.join('\\n')}`;\n\n  let next: string;\n  if (existing === null) {\n    next = `${block}\\n`;\n  } else {\n    const sep = existing.endsWith('\\n') ? '' : '\\n';\n    next = `${existing}${sep}${block}\\n`;\n  }\n\n  if (!dry) writeFileSync(filePath, next, 'utf8');\n\n  return {\n    path: filePath,\n    action: existing === null ? 'create' : 'update',\n    description: `add ${missing.length} gitignore line(s)`,\n    contents: next,\n  };\n}\n","import { lstatSync } from 'node:fs';\n\n/**\n * Setup writers refuse to write through symlinks: a repo could ship e.g. an\n * `AGENTS.md -> ~/.ssh/config` link and turn a marker-block upsert into a\n * clobber of a file outside the repo. Shell-rc writes are exempt by design —\n * dotfiles are commonly symlinked and the user explicitly opts into that write.\n */\nexport function isSymlink(filePath: string): boolean {\n  try {\n    return lstatSync(filePath).isSymbolicLink();\n  } catch {\n    return false;\n  }\n}\n","import { readFileSync, writeFileSync } from 'node:fs';\n\nimport type { AttributionEnv, ChangeResult } from '../types';\n\n/**\n * Write a Substrata env block to a shell rc file, delimited by markers so a\n * re-run replaces it in place rather than appending. Pure + dry-runnable.\n */\n\nconst BEGIN = '# >>> substrata >>>';\nconst END = '# <<< substrata <<<';\n\nfunction readIfExists(filePath: string): string | null {\n  try {\n    return readFileSync(filePath, 'utf8');\n  } catch {\n    return null;\n  }\n}\n\nfunction renderBlock(vars: AttributionEnv): string {\n  const lines: string[] = [BEGIN, '# Substrata agent attribution (managed; safe to edit values)'];\n  if (vars.actor) lines.push(`export SUBSTRATA_ACTOR=\"${vars.actor}\"`);\n  if (vars.model) lines.push(`export SUBSTRATA_MODEL=\"${vars.model}\"`);\n  if (vars.requester) lines.push(`export SUBSTRATA_REQUESTER=\"${vars.requester}\"`);\n  lines.push(END);\n  return lines.join('\\n');\n}\n\n/**\n * Insert or replace the Substrata env block in `rcPath`.\n * The block is delimited by stable markers; reruns replace in place.\n */\nexport function writeShellEnv(\n  rcPath: string,\n  vars: AttributionEnv,\n  dry: boolean = false,\n): ChangeResult {\n  const block = renderBlock(vars);\n  const existing = readIfExists(rcPath);\n\n  const markerRe = new RegExp(`${escapeRegExp(BEGIN)}[\\\\s\\\\S]*?${escapeRegExp(END)}`, 'm');\n\n  let next: string;\n  let action: ChangeResult['action'];\n\n  if (existing === null) {\n    next = `${block}\\n`;\n    action = 'create';\n  } else if (markerRe.test(existing)) {\n    const replaced = existing.replace(markerRe, block);\n    if (replaced === existing) {\n      return { path: rcPath, action: 'skip', description: 'env block already current' };\n    }\n    next = replaced;\n    action = 'update';\n  } else {\n    const sep = existing.endsWith('\\n') ? '' : '\\n';\n    next = `${existing}${sep}\\n${block}\\n`;\n    action = 'update';\n  }\n\n  if (!dry) writeFileSync(rcPath, next, 'utf8');\n\n  return {\n    path: rcPath,\n    action,\n    description: 'write Substrata env block',\n    contents: next,\n  };\n}\n\nfunction escapeRegExp(s: string): string {\n  return s.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\$&');\n}\n","import { readFileSync, writeFileSync } from 'node:fs';\nimport path from 'node:path';\n\nimport type { ChangeResult } from '../types';\nimport { isSymlink } from './symlink';\n\n/**\n * Insert/replace the Substrata section in AGENTS.md between begin/end markers.\n * Replace-in-place on rerun; never duplicates. Pure + dry-runnable. See plan §10.\n */\n\nconst BEGIN = '<!-- substrata:start -->';\nconst END = '<!-- substrata:end -->';\n\nexport const AGENTS_MD_SECTION = `${BEGIN}\n## Substrata Rules\n\nThis repository uses Substrata for shared agent memory.\n\nSet these once per agent session so footprints are attributed correctly:\n- \\`SUBSTRATA_ACTOR\\`     (e.g. \"claude-code\")\n- \\`SUBSTRATA_MODEL\\`     (e.g. \"claude-opus-4\")\n- \\`SUBSTRATA_REQUESTER\\` (falls back to git user.email)\n\nBefore making non-trivial changes:\n\n1. Run \\`substrata context \"<task description>\"\\`.\n2. Search for relevant files using \\`substrata search\\` or the MCP tool \\`substrata_context\\`.\n3. Respect prior architectural decisions unless the user explicitly asks to override them.\n\nAfter making non-trivial changes:\n\n1. Add a footprint with \\`substrata add\\` or MCP tool \\`substrata_add\\`.\n2. Include: purpose, requester, actor, files changed, decisions made, rejected\n   alternatives, implementation notes, commands run, memory learned, future agent guidance.\n3. If the work changes durable repo conventions, update \\`.substrata/memory/\\`.\n4. If the work reverses a prior decision, use \\`substrata supersede\\`.\n\nDo not store secrets, credentials, private keys, tokens, or sensitive user data in Substrata files.\n${END}`;\n\nfunction readIfExists(filePath: string): string | null {\n  try {\n    return readFileSync(filePath, 'utf8');\n  } catch {\n    return null;\n  }\n}\n\nfunction escapeRegExp(s: string): string {\n  return s.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\$&');\n}\n\n/** Upsert the Substrata section into `<cwd>/AGENTS.md`. */\nexport function upsertAgentsMd(cwd: string, dry: boolean = false): ChangeResult {\n  const filePath = path.join(cwd, 'AGENTS.md');\n  if (isSymlink(filePath)) {\n    return { path: filePath, action: 'skip', description: 'refused: AGENTS.md is a symlink' };\n  }\n  const existing = readIfExists(filePath);\n  const markerRe = new RegExp(`${escapeRegExp(BEGIN)}[\\\\s\\\\S]*?${escapeRegExp(END)}`, 'm');\n\n  let next: string;\n  let action: ChangeResult['action'];\n\n  if (existing === null) {\n    next = `${AGENTS_MD_SECTION}\\n`;\n    action = 'create';\n  } else if (markerRe.test(existing)) {\n    const replaced = existing.replace(markerRe, AGENTS_MD_SECTION);\n    if (replaced === existing) {\n      return { path: filePath, action: 'skip', description: 'AGENTS.md section already current' };\n    }\n    next = replaced;\n    action = 'update';\n  } else {\n    const sep = existing.endsWith('\\n') ? '' : '\\n';\n    next = `${existing}${sep}\\n${AGENTS_MD_SECTION}\\n`;\n    action = 'update';\n  }\n\n  if (!dry) writeFileSync(filePath, next, 'utf8');\n\n  return {\n    path: filePath,\n    action,\n    description: 'write Substrata AGENTS.md section',\n    contents: next,\n  };\n}\n","import { chmodSync, readFileSync, writeFileSync } from 'node:fs';\nimport path from 'node:path';\n\nimport type { ChangeResult } from '../types';\nimport { isSymlink } from './symlink';\n\n/**\n * Install a pre-commit hook that runs the Substrata staged-file secret scan as a\n * second line of defense. If a hook already exists, append a guarded block\n * rather than clobbering it. Pure-ish + dry-runnable. See plan §8.11/§12.\n */\n\nconst GUARD_BEGIN = '# >>> substrata pre-commit >>>';\nconst GUARD_END = '# <<< substrata pre-commit <<<';\n\nconst GUARDED_BLOCK = `${GUARD_BEGIN}\n# Substrata secret scan over staged .substrata files (second line of defense).\nnpx --no-install substrata internal-scan-staged || exit 1\n${GUARD_END}`;\n\nconst FULL_HOOK = `#!/bin/sh\n${GUARDED_BLOCK}\n`;\n\nfunction readIfExists(filePath: string): string | null {\n  try {\n    return readFileSync(filePath, 'utf8');\n  } catch {\n    return null;\n  }\n}\n\n/** Install/refresh the pre-commit hook at `<cwd>/.git/hooks/pre-commit`. */\nexport function installSecretHook(cwd: string, dry: boolean = false): ChangeResult {\n  const filePath = path.join(cwd, '.git', 'hooks', 'pre-commit');\n  if (isSymlink(filePath)) {\n    return { path: filePath, action: 'skip', description: 'refused: pre-commit hook is a symlink' };\n  }\n  const existing = readIfExists(filePath);\n\n  let next: string;\n  let action: ChangeResult['action'];\n\n  if (existing === null) {\n    next = FULL_HOOK;\n    action = 'create';\n  } else if (existing.includes(GUARD_BEGIN)) {\n    return { path: filePath, action: 'skip', description: 'pre-commit hook already installed' };\n  } else {\n    const sep = existing.endsWith('\\n') ? '' : '\\n';\n    next = `${existing}${sep}\\n${GUARDED_BLOCK}\\n`;\n    action = 'update';\n  }\n\n  if (!dry) {\n    writeFileSync(filePath, next, 'utf8');\n    chmodSync(filePath, 0o755);\n  }\n\n  return {\n    path: filePath,\n    action,\n    description: 'install Substrata pre-commit secret hook',\n    contents: next,\n  };\n}\n","import type { ChangeResult } from '../types';\n\n/**\n * Aggregate ChangeResults into a printable setup plan. Pure (no I/O).\n */\n\nconst ACTION_LABEL: Record<ChangeResult['action'], string> = {\n  create: 'CREATE',\n  update: 'UPDATE',\n  skip: 'SKIP  ',\n};\n\n/** Render a list of changes as aligned, human-readable plan lines. */\nexport function renderPlan(changes: ChangeResult[]): string {\n  if (changes.length === 0) return 'No changes.';\n  return changes\n    .map((c) => `${ACTION_LABEL[c.action]}  ${c.path}${c.description ? ` — ${c.description}` : ''}`)\n    .join('\\n');\n}\n\n/** True if any change actually writes (create/update). */\nexport function hasEffectiveChanges(changes: ChangeResult[]): boolean {\n  return changes.some((c) => c.action !== 'skip');\n}\n\n/** Summary counts by action, e.g. for a plan footer. */\nexport function summarizePlan(changes: ChangeResult[]): {\n  create: number;\n  update: number;\n  skip: number;\n} {\n  const summary = { create: 0, update: 0, skip: 0 };\n  for (const c of changes) summary[c.action] += 1;\n  return summary;\n}\n","import { stat } from 'node:fs/promises';\n\nimport {\n  listFootprints,\n  listMemoryDocuments,\n  relativeToCwd,\n  type Footprint,\n  type MemoryDocument,\n} from '@substrata/core';\nimport type Database from 'better-sqlite3';\n\nimport { applySchema, dropSchema, SCHEMA_VERSION } from './schema';\nimport { closeDb, openIndexDb } from './sqlite';\n\nexport type BuildIndexOptions = {\n  /**\n   * Reserved for API symmetry with the plan signature. The MVP performs a full\n   * rebuild on every call (drop & recreate rows), so this flag is a no-op today\n   * but kept so callers can pass it without breaking.\n   */\n  rebuild?: boolean;\n};\n\n/** Row shape inserted into the `documents` table. */\ntype DocumentRow = {\n  id: string;\n  type: 'footprint' | 'memory';\n  title: string;\n  filePath: string;\n  status: string | null;\n  createdAt: string | null;\n  updatedAt: string | null;\n  tags: string[];\n  files: string[];\n  /** Full searchable content (joined sections / body). */\n  content: string;\n  workType: string | null;\n};\n\nfunction joinNonEmpty(parts: Array<string | undefined | null>): string {\n  return parts\n    .map((p) => (p ?? '').trim())\n    .filter((p) => p.length > 0)\n    .join('\\n\\n');\n}\n\n/** Flatten a footprint into a single searchable document row. */\nfunction footprintToRow(cwd: string, fp: Footprint): DocumentRow {\n  const fm = fp.frontmatter;\n  const s = fp.sections;\n\n  const rejected = (s.rejectedOptions ?? []).map((r) => `${r.option}: ${r.reason}`).join('\\n');\n\n  const content = joinNonEmpty([\n    fp.title,\n    s.purpose,\n    (s.decisions ?? []).join('\\n'),\n    rejected,\n    s.implementationNotes,\n    (s.memoryLearned ?? []).join('\\n'),\n    s.futureAgentGuidance,\n    (fm.tags ?? []).join(' '),\n    (fm.files_touched ?? []).join(' '),\n  ]);\n\n  return {\n    id: fm.id,\n    type: 'footprint',\n    title: fp.title,\n    filePath: relativeToCwd(cwd, fp.filePath),\n    status: fm.status,\n    createdAt: fm.created_at,\n    updatedAt: fm.updated_at ?? null,\n    tags: fm.tags ?? [],\n    files: fm.files_touched ?? [],\n    content,\n    workType: fm.work_type,\n  };\n}\n\n/** Flatten a memory document into a single searchable document row. */\nfunction memoryToRow(cwd: string, doc: MemoryDocument): DocumentRow {\n  const fm = doc.frontmatter;\n  const tags = Array.isArray(fm.tags) ? fm.tags : [];\n\n  const content = joinNonEmpty([doc.title, doc.body, tags.join(' ')]);\n\n  return {\n    id: fm.id,\n    type: 'memory',\n    title: doc.title,\n    filePath: relativeToCwd(cwd, doc.filePath),\n    status: null,\n    createdAt: null,\n    updatedAt: typeof fm.updated_at === 'string' ? fm.updated_at : null,\n    tags,\n    files: [],\n    content,\n    workType: null,\n  };\n}\n\nasync function maxMtimeMs(filePaths: string[]): Promise<number> {\n  let max = 0;\n  for (const filePath of filePaths) {\n    try {\n      const st = await stat(filePath);\n      if (st.mtimeMs > max) max = st.mtimeMs;\n    } catch {\n      // file vanished between listing and stat; ignore.\n    }\n  }\n  return max;\n}\n\nfunction writeRows(db: Database.Database, rows: DocumentRow[]): void {\n  const insertDoc = db.prepare(\n    `INSERT INTO documents\n       (id, type, title, file_path, status, created_at, updated_at, tags_json, files_json, raw_text, work_type)\n     VALUES\n       (@id, @type, @title, @filePath, @status, @createdAt, @updatedAt, @tagsJson, @filesJson, @content, @workType)`,\n  );\n  const insertFts = db.prepare(\n    `INSERT INTO documents_fts (id, title, tags, files, content)\n     VALUES (@id, @title, @tags, @files, @content)`,\n  );\n\n  for (const row of rows) {\n    insertDoc.run({\n      id: row.id,\n      type: row.type,\n      title: row.title,\n      filePath: row.filePath,\n      status: row.status,\n      createdAt: row.createdAt,\n      updatedAt: row.updatedAt,\n      tagsJson: JSON.stringify(row.tags),\n      filesJson: JSON.stringify(row.files),\n      content: row.content,\n      workType: row.workType,\n    });\n    insertFts.run({\n      id: row.id,\n      title: row.title,\n      tags: row.tags.join(' '),\n      files: row.files.join(' '),\n      content: row.content,\n    });\n  }\n}\n\nfunction writeMeta(\n  db: Database.Database,\n  meta: { sourceMaxMtime: number; sourceFileCount: number },\n): void {\n  const upsert = db.prepare(\n    `INSERT INTO index_meta (key, value) VALUES (@key, @value)\n     ON CONFLICT(key) DO UPDATE SET value = excluded.value`,\n  );\n  upsert.run({ key: 'schema_version', value: String(SCHEMA_VERSION) });\n  upsert.run({ key: 'built_at', value: new Date().toISOString() });\n  upsert.run({ key: 'source_max_mtime', value: String(meta.sourceMaxMtime) });\n  upsert.run({ key: 'source_file_count', value: String(meta.sourceFileCount) });\n}\n\n/**\n * Build (or fully rebuild) the search index for `cwd`. Loads footprints and\n * memory documents via `@substrata/core`, flattens each into one searchable\n * `documents` + `documents_fts` row, and records freshness metadata. The MVP\n * always does a full rebuild (drop & recreate rows) inside a transaction.\n */\nexport async function buildIndex(cwd: string, _options: BuildIndexOptions = {}): Promise<void> {\n  const [footprints, memory] = await Promise.all([listFootprints(cwd), listMemoryDocuments(cwd)]);\n\n  const rows: DocumentRow[] = [\n    ...footprints.map((fp) => footprintToRow(cwd, fp)),\n    ...memory.map((doc) => memoryToRow(cwd, doc)),\n  ];\n\n  const sourceFiles = [\n    ...footprints.map((fp) => fp.filePath),\n    ...memory.map((doc) => doc.filePath),\n  ];\n  const sourceMaxMtime = await maxMtimeMs(sourceFiles);\n\n  const db = openIndexDb(cwd);\n  try {\n    const rebuild = db.transaction(() => {\n      // Full rebuild: drop & recreate so a schema bump or removed source files\n      // never leave stale rows behind.\n      dropSchema(db);\n      applySchema(db);\n      writeRows(db, rows);\n      writeMeta(db, { sourceMaxMtime, sourceFileCount: sourceFiles.length });\n    });\n    rebuild();\n  } finally {\n    closeDb(db);\n  }\n}\n","import type Database from 'better-sqlite3';\n\n/**\n * SQLite index schema. See plan §11 (\"SQLite schema\").\n *\n * `documents` holds the structured row (for filtering + ranking inputs);\n * `documents_fts` is the FTS5 virtual table queried via MATCH; `index_meta`\n * carries freshness metadata (schema_version, built_at, source_max_mtime,\n * source_file_count) so the index can be detected as missing/stale/fresh\n * without re-parsing source files.\n */\n\n/** Bump when the schema or indexing semantics change. */\nexport const SCHEMA_VERSION = 1;\n\nconst CREATE_DOCUMENTS = `\nCREATE TABLE IF NOT EXISTS documents (\n  id TEXT PRIMARY KEY,\n  type TEXT NOT NULL,\n  title TEXT NOT NULL,\n  file_path TEXT NOT NULL,\n  status TEXT,\n  created_at TEXT,\n  updated_at TEXT,\n  tags_json TEXT NOT NULL,\n  files_json TEXT NOT NULL,\n  raw_text TEXT NOT NULL,\n  work_type TEXT\n);\n`;\n\nconst CREATE_DOCUMENTS_FTS = `\nCREATE VIRTUAL TABLE IF NOT EXISTS documents_fts USING fts5(\n  id UNINDEXED,\n  title,\n  tags,\n  files,\n  content,\n  tokenize = 'porter unicode61'\n);\n`;\n\nconst CREATE_INDEX_META = `\nCREATE TABLE IF NOT EXISTS index_meta (\n  key   TEXT PRIMARY KEY,\n  value TEXT NOT NULL\n);\n`;\n\n/** Create all tables if they do not already exist. Idempotent. */\nexport function applySchema(db: Database.Database): void {\n  db.exec(CREATE_DOCUMENTS);\n  db.exec(CREATE_DOCUMENTS_FTS);\n  db.exec(CREATE_INDEX_META);\n}\n\n/** Drop all index tables (used by a full rebuild). */\nexport function dropSchema(db: Database.Database): void {\n  db.exec('DROP TABLE IF EXISTS documents;');\n  db.exec('DROP TABLE IF EXISTS documents_fts;');\n  db.exec('DROP TABLE IF EXISTS index_meta;');\n}\n","import { existsSync, mkdirSync } from 'node:fs';\nimport path from 'node:path';\n\nimport { indexPath } from '@substrata/core';\nimport Database from 'better-sqlite3';\n\nimport { applySchema } from './schema';\n\nexport type OpenIndexDbOptions = {\n  /** Open the existing DB read-only; never create or migrate. */\n  readonly?: boolean;\n};\n\n/**\n * Open (or create) the SQLite index database at `@substrata/core`'s\n * `indexPath(cwd)`. The parent `index/` directory is created if missing.\n *\n * In read-only mode the DB must already exist (better-sqlite3 will throw\n * otherwise); the schema is left untouched. In read-write mode the schema is\n * applied idempotently so a freshly created file is immediately usable.\n */\nexport function openIndexDb(cwd: string, options: OpenIndexDbOptions = {}): Database.Database {\n  const dbPath = indexPath(cwd);\n\n  if (!options.readonly) {\n    mkdirSync(path.dirname(dbPath), { recursive: true });\n  }\n\n  const db = new Database(dbPath, { readonly: options.readonly ?? false });\n\n  if (!options.readonly) {\n    db.pragma('journal_mode = DELETE');\n    applySchema(db);\n  }\n\n  return db;\n}\n\n/** True when an index database file exists on disk for `cwd`. */\nexport function indexDbExists(cwd: string): boolean {\n  return existsSync(indexPath(cwd));\n}\n\n/** Close a database handle, ignoring errors from an already-closed handle. */\nexport function closeDb(db: Database.Database): void {\n  try {\n    db.close();\n  } catch {\n    // already closed; nothing to do.\n  }\n}\n","import type { Dirent } from 'node:fs';\nimport { readdir, stat } from 'node:fs/promises';\nimport path from 'node:path';\n\nimport { footprintsDir, memoryDir, type IndexStatus } from '@substrata/core';\n\nimport { SCHEMA_VERSION } from './schema';\nimport { closeDb, indexDbExists, openIndexDb } from './sqlite';\n\n/**\n * Cheap stat walk of the footprint/memory dirs: collect the max mtime (ms) and\n * the count of `.md` files. No file contents are read or parsed — this mirrors\n * what `buildIndex` records so freshness can be checked without re-indexing.\n */\nasync function walkStats(dir: string): Promise<{ maxMtime: number; count: number }> {\n  let entries: Dirent[];\n  try {\n    entries = await readdir(dir, { withFileTypes: true });\n  } catch {\n    return { maxMtime: 0, count: 0 };\n  }\n\n  let maxMtime = 0;\n  let count = 0;\n  for (const entry of entries) {\n    const full = path.join(dir, entry.name);\n    if (entry.isDirectory()) {\n      const sub = await walkStats(full);\n      if (sub.maxMtime > maxMtime) maxMtime = sub.maxMtime;\n      count += sub.count;\n    } else if (entry.isFile() && entry.name.endsWith('.md')) {\n      count += 1;\n      try {\n        const st = await stat(full);\n        if (st.mtimeMs > maxMtime) maxMtime = st.mtimeMs;\n      } catch {\n        // ignore unreadable file\n      }\n    }\n  }\n  return { maxMtime, count };\n}\n\nfunction readMeta(cwd: string): Map<string, string> {\n  const db = openIndexDb(cwd, { readonly: true });\n  try {\n    const rows = db.prepare('SELECT key, value FROM index_meta').all() as Array<{\n      key: string;\n      value: string;\n    }>;\n    return new Map(rows.map((r) => [r.key, r.value]));\n  } finally {\n    closeDb(db);\n  }\n}\n\n/**\n * Report whether the on-disk index is missing, stale, or fresh for `cwd`.\n *\n * - missing: no index DB file on disk.\n * - stale/schema: recorded schema_version differs from the current one.\n * - stale/count: the source `.md` file count changed.\n * - stale/mtime: a source file is newer than the recorded build mtime.\n * - fresh: otherwise.\n *\n * Comparison is against a cheap stat walk only (plan §11) — no parsing.\n */\nexport async function getIndexStatus(cwd: string): Promise<IndexStatus> {\n  if (!indexDbExists(cwd)) {\n    return { state: 'missing' };\n  }\n\n  let meta: Map<string, string>;\n  try {\n    meta = readMeta(cwd);\n  } catch {\n    // Corrupt or unreadable DB — treat as missing so callers rebuild.\n    return { state: 'missing' };\n  }\n\n  const recordedSchema = Number(meta.get('schema_version'));\n  if (!Number.isFinite(recordedSchema) || recordedSchema !== SCHEMA_VERSION) {\n    return { state: 'stale', reason: 'schema' };\n  }\n\n  const [fp, mem] = await Promise.all([walkStats(footprintsDir(cwd)), walkStats(memoryDir(cwd))]);\n  const sourceCount = fp.count + mem.count;\n  const sourceMaxMtime = Math.max(fp.maxMtime, mem.maxMtime);\n\n  const recordedCount = Number(meta.get('source_file_count'));\n  if (!Number.isFinite(recordedCount) || recordedCount !== sourceCount) {\n    return { state: 'stale', reason: 'count' };\n  }\n\n  const recordedMtime = Number(meta.get('source_max_mtime'));\n  // Allow a 1ms tolerance for filesystem mtime granularity differences.\n  if (!Number.isFinite(recordedMtime) || sourceMaxMtime > recordedMtime + 1) {\n    return { state: 'stale', reason: 'mtime' };\n  }\n\n  return { state: 'fresh' };\n}\n","import path from 'node:path';\n\nimport { toPosix, type FootprintStatus, type SearchResult, type WorkType } from '@substrata/core';\nimport type Database from 'better-sqlite3';\n\nimport { score } from './ranking';\nimport { closeDb, openIndexDb } from './sqlite';\n\nexport type SearchOptions = {\n  cwd: string;\n  limit?: number;\n  /** Hard filter: only docs whose files_touched include one of these. */\n  files?: string[];\n  /** Hard filter: only docs carrying one of these tags. */\n  tags?: string[];\n  /** Drop superseded AND deprecated docs entirely. */\n  excludeSuperseded?: boolean;\n};\n\nconst DEFAULT_LIMIT = 8;\n\n/**\n * Baseline relevance assigned to a direct file-hit in `getRelatedToFile` (these\n * rows do not come from an FTS MATCH, so they have no bm25). Chosen negative\n * (bm25 convention: lower is better) so a strong file match ranks comparably to\n * a good text match before the ×1.5 file-overlap boost is applied.\n */\nconst FILE_HIT_BM25 = -10;\n\n/** Row joined from documents + the FTS match. */\ntype JoinedRow = {\n  id: string;\n  type: string;\n  title: string;\n  file_path: string;\n  status: string | null;\n  created_at: string | null;\n  updated_at: string | null;\n  tags_json: string;\n  files_json: string;\n  work_type: string | null;\n  bm25: number;\n  snippet: string;\n};\n\nfunction parseJsonArray(value: string): string[] {\n  try {\n    const parsed = JSON.parse(value);\n    return Array.isArray(parsed) ? (parsed as string[]) : [];\n  } catch {\n    return [];\n  }\n}\n\n/**\n * Build a safe FTS5 MATCH expression from free-form user text. Each token is\n * wrapped in double quotes (with internal quotes doubled) so user punctuation\n * (e.g. `?!`, `:`, `-`) can never be interpreted as FTS5 query syntax. Tokens\n * are OR-ed so natural-language queries (e.g. \"why did we avoid Redis?!\") still\n * recall the relevant docs; ranking then orders by relevance. Returns null when\n * the query has no usable tokens.\n */\nexport function buildMatchQuery(query: string): string | null {\n  const tokens = query\n    .split(/[^A-Za-z0-9_]+/u)\n    .map((t) => t.trim())\n    .filter((t) => t.length > 0);\n  if (tokens.length === 0) return null;\n  return tokens.map((t) => `\"${t.replace(/\"/g, '\"\"')}\"`).join(' OR ');\n}\n\nfunction rowToResult(row: JoinedRow, queryFiles: string[]): SearchResult {\n  const tags = parseJsonArray(row.tags_json);\n  const files = parseJsonArray(row.files_json);\n  const status = (row.status ?? 'completed') as FootprintStatus;\n\n  const ranked = score(\n    {\n      bm25: row.bm25,\n      status: row.status as FootprintStatus | null,\n      workType: row.work_type as WorkType | null,\n      updatedAt: row.updated_at,\n      createdAt: row.created_at,\n      docFiles: files,\n      queryFiles,\n    },\n    Date.now(),\n  );\n\n  return {\n    id: row.id,\n    title: row.title,\n    filePath: row.file_path,\n    score: ranked,\n    snippet: row.snippet,\n    tags,\n    createdAt: row.created_at ?? undefined,\n    filesTouched: files,\n    status,\n  };\n}\n\ntype ExecuteOptions = {\n  excludeSuperseded?: boolean;\n  files?: string[];\n  tags?: string[];\n  limit: number;\n};\n\n/**\n * Run a MATCH query against an open DB, apply hard tag/file/status filters in\n * SQL, then rank + sort in JS. Shared by `search` and `getRelatedToFile`.\n */\nfunction executeMatch(\n  db: Database.Database,\n  match: string,\n  queryFiles: string[],\n  options: ExecuteOptions,\n): SearchResult[] {\n  const where: string[] = [];\n  const params: Record<string, unknown> = { match };\n\n  if (options.excludeSuperseded) {\n    // Memory docs have NULL status and are always kept; only footprint statuses\n    // superseded/deprecated are dropped.\n    where.push(\"(d.status IS NULL OR d.status NOT IN ('superseded', 'deprecated'))\");\n  }\n\n  if (options.tags && options.tags.length > 0) {\n    const clauses = options.tags.map((tag, i) => {\n      params[`tag${i}`] = tag;\n      return `EXISTS (SELECT 1 FROM json_each(d.tags_json) WHERE json_each.value = @tag${i})`;\n    });\n    where.push(`(${clauses.join(' OR ')})`);\n  }\n\n  if (options.files && options.files.length > 0) {\n    const clauses = options.files.map((file, i) => {\n      params[`file${i}`] = toPosix(file);\n      return `EXISTS (SELECT 1 FROM json_each(d.files_json) WHERE json_each.value = @file${i})`;\n    });\n    where.push(`(${clauses.join(' OR ')})`);\n  }\n\n  const whereSql = where.length > 0 ? ` AND ${where.join(' AND ')}` : '';\n\n  const sql = `\n    SELECT\n      d.id, d.type, d.title, d.file_path, d.status,\n      d.created_at, d.updated_at, d.tags_json, d.files_json, d.work_type,\n      bm25(documents_fts) AS bm25,\n      snippet(documents_fts, 4, '[', ']', ' … ', 12) AS snippet\n    FROM documents_fts\n    JOIN documents d ON d.id = documents_fts.id\n    WHERE documents_fts MATCH @match${whereSql}\n  `;\n\n  const rows = db.prepare(sql).all(params) as JoinedRow[];\n  const results = rows.map((row) => rowToResult(row, queryFiles));\n  results.sort((a, b) => b.score - a.score);\n  return results.slice(0, options.limit);\n}\n\n/**\n * Full-text search over footprints + memory. Builds a safe MATCH expression,\n * applies hard tag/file filters and optional superseded exclusion, ranks per\n * plan §11, and returns up to `limit` results.\n */\nexport async function search(query: string, options: SearchOptions): Promise<SearchResult[]> {\n  const limit = options.limit ?? DEFAULT_LIMIT;\n  const match = buildMatchQuery(query);\n  if (!match) return [];\n\n  const queryFiles = (options.files ?? []).map((f) => toPosix(f));\n\n  const db = openIndexDb(options.cwd, { readonly: true });\n  try {\n    return executeMatch(db, match, queryFiles, {\n      excludeSuperseded: options.excludeSuperseded,\n      files: options.files,\n      tags: options.tags,\n      limit,\n    });\n  } finally {\n    closeDb(db);\n  }\n}\n\n/**\n * Find footprints/memory related to a specific file. Primary signal is a doc\n * whose `files_json` contains the posix-normalized path; an FTS fallback on the\n * filename stem broadens recall. Results are merged (dedup by id, file-hit\n * preferred) and ranked by the same rules.\n */\nexport async function getRelatedToFile(\n  filePath: string,\n  options: SearchOptions,\n): Promise<SearchResult[]> {\n  const limit = options.limit ?? DEFAULT_LIMIT;\n  const posixPath = toPosix(filePath);\n  const stem = path.basename(posixPath).replace(/\\.[^.]+$/, '');\n\n  const db = openIndexDb(options.cwd, { readonly: true });\n  try {\n    // Hard file matches: docs whose files_touched contain the exact path.\n    const fileRows = db\n      .prepare(\n        `SELECT\n           d.id, d.type, d.title, d.file_path, d.status,\n           d.created_at, d.updated_at, d.tags_json, d.files_json, d.work_type\n         FROM documents d\n         WHERE EXISTS (\n           SELECT 1 FROM json_each(d.files_json) WHERE json_each.value = @path\n         )`,\n      )\n      .all({ path: posixPath }) as Omit<JoinedRow, 'bm25' | 'snippet'>[];\n\n    const byId = new Map<string, SearchResult>();\n    for (const row of fileRows) {\n      const joined: JoinedRow = { ...row, bm25: FILE_HIT_BM25, snippet: '' };\n      // The file hit counts as overlap automatically: queryFiles includes\n      // posixPath, so rowToResult applies the ×1.5 boost via the ranker.\n      const result = rowToResult(joined, [posixPath]);\n      byId.set(result.id, result);\n    }\n\n    // FTS fallback on the filename stem to broaden recall.\n    const match = buildMatchQuery(stem);\n    if (match) {\n      const ftsResults = executeMatch(db, match, [posixPath], {\n        excludeSuperseded: options.excludeSuperseded,\n        tags: options.tags,\n        limit: limit * 4,\n      });\n      for (const r of ftsResults) {\n        if (!byId.has(r.id)) byId.set(r.id, r);\n      }\n    }\n\n    let merged = Array.from(byId.values());\n    if (options.excludeSuperseded) {\n      merged = merged.filter((r) => r.status !== 'superseded' && r.status !== 'deprecated');\n    }\n    merged.sort((a, b) => b.score - a.score);\n    return merged.slice(0, limit);\n  } finally {\n    closeDb(db);\n  }\n}\n","import type { FootprintStatus, WorkType } from '@substrata/core';\n\n/**\n * Ranking helpers. See plan §11 (\"Ranking (MVP)\").\n *\n * All helpers are pure so they can be unit-tested in isolation. `score` applies\n * the full pipeline: BM25 → normalize → multiplicative boosts → status penalty.\n */\n\n/** Days over which the recency boost decays linearly from 1 to 0. */\nexport const RECENCY_DECAY_DAYS = 180;\nconst MS_PER_DAY = 24 * 60 * 60 * 1000;\n\n/** Maximum fractional recency boost (plan: × (1 + 0.15 * decay)). */\nexport const RECENCY_BOOST_WEIGHT = 0.15;\n\n/** Multiplier when the doc's files overlap the queried files. */\nexport const FILES_OVERLAP_BOOST = 1.5;\n\n/** Multiplicative status penalties (plan §11 step 4). */\nexport const STATUS_PENALTIES: Record<FootprintStatus, number> = {\n  draft: 0.5,\n  completed: 1,\n  superseded: 0.15,\n  deprecated: 0.1,\n};\n\n/**\n * better-sqlite3's fts5 `bm25()` returns a score where *more negative is more\n * relevant*. Normalize to a positive relevance value so boosts/penalties read\n * naturally (higher = better).\n */\nexport function normalizeBm25(bm25: number): number {\n  return -bm25;\n}\n\n/**\n * Linear recency decay in [0, 1]: 1 for \"now\", decaying to 0 at\n * RECENCY_DECAY_DAYS old and clamped at 0 beyond that. A missing/invalid date\n * yields 0 (no recency contribution).\n */\nexport function recencyDecay(timestamp: string | undefined, now: number = Date.now()): number {\n  if (!timestamp) return 0;\n  const t = Date.parse(timestamp);\n  if (Number.isNaN(t)) return 0;\n  const ageDays = (now - t) / MS_PER_DAY;\n  if (ageDays <= 0) return 1;\n  if (ageDays >= RECENCY_DECAY_DAYS) return 0;\n  return 1 - ageDays / RECENCY_DECAY_DAYS;\n}\n\n/**\n * Recency boost multiplier: × (1 + weight * decay). For\n * `architecture_decision`, the boost contribution is halved so durable\n * decisions are not demoted merely for being old.\n */\nexport function recencyBoost(\n  timestamp: string | undefined,\n  workType: WorkType | null | undefined,\n  now: number = Date.now(),\n): number {\n  let contribution = RECENCY_BOOST_WEIGHT * recencyDecay(timestamp, now);\n  if (workType === 'architecture_decision') {\n    contribution /= 2;\n  }\n  return 1 + contribution;\n}\n\n/** True when any of the doc's files matches any queried file (case-insensitive). */\nexport function filesOverlap(docFiles: string[], queryFiles: string[]): boolean {\n  if (queryFiles.length === 0 || docFiles.length === 0) return false;\n  const want = new Set(queryFiles.map((f) => f.toLowerCase()));\n  return docFiles.some((f) => want.has(f.toLowerCase()));\n}\n\n/** Multiplicative status penalty; unknown/undefined status is treated as neutral. */\nexport function statusPenalty(status: FootprintStatus | null | undefined): number {\n  if (!status) return 1;\n  return STATUS_PENALTIES[status] ?? 1;\n}\n\nexport type RankInput = {\n  bm25: number;\n  status?: FootprintStatus | null;\n  workType?: WorkType | null;\n  /** updated_at ?? created_at, used for recency. */\n  updatedAt?: string | null;\n  createdAt?: string | null;\n  docFiles: string[];\n  queryFiles: string[];\n};\n\n/**\n * Full ranking score: normalized BM25 with multiplicative file-overlap,\n * recency, and status modifiers applied per plan §11.\n */\nexport function score(input: RankInput, now: number = Date.now()): number {\n  let s = normalizeBm25(input.bm25);\n\n  if (filesOverlap(input.docFiles, input.queryFiles)) {\n    s *= FILES_OVERLAP_BOOST;\n  }\n\n  const recencyTimestamp = input.updatedAt ?? input.createdAt ?? undefined;\n  s *= recencyBoost(recencyTimestamp, input.workType ?? null, now);\n\n  s *= statusPenalty(input.status ?? null);\n\n  return 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