deepseek-harness/scripts/gen-doc-graphs.ts

/**
 * Generate (and verify) the relationship-diagram docs.
 *
 * This is the relationship layer above the existing catalogs:
 * - module-graph.md answers "which packages depend on which packages?"
 * - cordis-catalog/ answers "which events and services exist?"
 * - tool-catalog.md answers "which tools does the model see?"
 * - generated relationship diagrams answer "how do those pieces fit together?"
 *
 * Generated pages discover the enumerable facts from source. Hybrid pages use
 * discovered inventory plus small manifests for policy that source cannot infer
 * (for example, whether a package is an implementation or consumer in a seam).
 * Curated pages are still emitted here so the graph docs are one regenerated unit,
 * but their diagrams intentionally explain flow and ownership rather than
 * pretending to enumerate every source edge.
 *
 *   `tsx scripts/gen-doc-graphs.ts`          -> write generated diagram docs
 *   `tsx scripts/gen-doc-graphs.ts --check`  -> exit 1 if any file is stale
 */

import { existsSync, globSync, mkdirSync, readFileSync, writeFileSync } from 'node:fs'
import { dirname, relative, resolve } from 'node:path'
import ts from 'typescript'
import { collectEvents, collectServices } from './gen-cordis-catalog.ts'

const root = resolve(import.meta.dirname, '..')
const SCOPE = '@deepseek-ai/dsh-'

interface PkgJson {
  name: string
  peerDependencies?: Record<string, string>
}

interface Pkg {
  short: string
  name: string
  group: string
  rel: string
  deps: string[]
}

interface GraphDoc {
  rel: string
  content: string
}

interface ServiceRole {
  key: string
  pkg: string
  title: string
  mode: 'core' | 'seam' | 'bundle'
  implementations?: string[]
  consumers?: string[]
  companions?: string[]
  note: string
}

interface ExamplePlugin {
  id: string
  name: string
}

interface EventRelation {
  dispatchers: Map<string, Set<string>>
  listeners: Set<string>
}

const GROUP_ORDER = [
  'util',
  'llm',
  'core',
  'bash',
  'fs',
  'compact',
  'subagent',
  'web',
  'todo',
  'cordis',
  'hooks',
  'session-persistence',
  'session-query',
  'support',
  'ui',
]

const SERVICE_ROLES: ServiceRole[] = [
  {
    key: 'llm',
    pkg: 'llm',
    title: 'LLM adapter registry',
    mode: 'seam',
    implementations: ['llm-deepseek', 'llm-pi-ai', 'llm-replay'],
    consumers: ['agent-loop', 'compact-basic'],
    note: 'Adapters register provider implementations; the loop and compaction call the provider-neutral stream service.',
  },
  {
    key: 'sessions',
    pkg: 'session',
    title: 'In-memory session store',
    mode: 'core',
    consumers: ['agent-loop', 'agent', 'session-persistence', 'session-query', 'subagent-inprocess', 'invariants'],
    note: 'Owns append-only Session instances and emits the durable session event feed.',
  },
  {
    key: 'sessionPersistence',
    pkg: 'session-persistence',
    title: 'Durable session persistence seam',
    mode: 'seam',
    implementations: ['session-persistence-jsonl', 'session-persistence-sqlite'],
    consumers: ['agent-loop', 'acp', 'session-query'],
    note: 'Backends persist the same SessionEvent vocabulary; apps choose a backend at composition time.',
  },
  {
    key: 'sessionQuery',
    pkg: 'session-query',
    title: 'Session retrieval read model',
    mode: 'seam',
    note: 'Resolves live and optional persisted logs into one corpus and coordinates registered full-text providers.',
  },
  {
    key: 'systemPrompt',
    pkg: 'system-prompt',
    title: 'System prompt assembly registry',
    mode: 'core',
    consumers: ['agent-loop', 'tools', 'tool-fs', 'tool-web'],
    note: 'Collects prompt sections and model-facing tool schemas for each step.',
  },
  {
    key: 'tools',
    pkg: 'tools',
    title: 'Tool registry and execution waterfall',
    mode: 'core',
    consumers: ['agent-loop', 'tool-ask-user', 'tool-bash', 'tool-cordis', 'tool-fs', 'tool-subagent', 'tool-todo', 'tool-web', 'acp'],
    note: 'Registers tool definitions, exposes schemas to the prompt, and routes calls through tools/pre-execute and tools/post-execute.',
  },
  {
    key: 'userInteraction',
    pkg: 'user-interaction',
    title: 'Human question/answer seam',
    mode: 'seam',
    implementations: ['stdio-agent', 'acp'],
    consumers: ['tool-ask-user', 'stdio-agent', 'acp'],
    note: 'UI front doors provide the active human-answer provider; tool-ask-user pauses a tool call on the provider-neutral ask() promise.',
  },
  {
    key: 'agents',
    pkg: 'agent',
    title: 'Agent registry',
    mode: 'core',
    consumers: ['agent-loop', 'acp', 'subagent-inprocess', 'stdio-agent', 'invariants'],
    note: 'Owns live Agent handles and the create/resume factory seam.',
  },
  {
    key: 'agentLoop',
    pkg: 'agent-loop',
    title: 'Concrete loop driver',
    mode: 'bundle',
    consumers: ['agent-core'],
    note: 'The one concrete loop plugin; extension packages depend on dsh-agent events and services, not on this package.',
  },
  {
    key: 'bash',
    pkg: 'bash',
    title: 'Bash executor seam',
    mode: 'seam',
    implementations: ['bash-local'],
    consumers: ['tool-bash', 'hooks-claude', 'hooks-codex'],
    note: 'The model-facing bash tools and hook bridges consume this seam; sandboxed or remote executors can replace bash-local.',
  },
  {
    key: 'codeRuntime',
    pkg: 'code-runtime',
    title: 'Code-execution seam',
    mode: 'seam',
    implementations: ['code-runtime-worker'],
    consumers: ['tools'],
    note: 'Runs one model-written program against host-provided async bindings; backends differ by substrate and language (the tool registry consumes it for Code Mode).',
  },
  {
    key: 'fs',
    pkg: 'fs',
    title: 'Filesystem provider seam',
    mode: 'seam',
    implementations: ['fs-local'],
    consumers: ['tool-fs'],
    companions: ['fs-policy'],
    note: 'tool-fs executes read/write/edit through ctx.fs; fs-policy contributes observed-state checks through the fs/* event gate.',
  },
  {
    key: 'compact',
    pkg: 'compact',
    title: 'Compaction seam',
    mode: 'seam',
    implementations: ['compact-basic'],
    consumers: ['compact-basic'],
    note: 'The basic backend currently consumes the pre-step event directly; a model-facing compact tool remains deferred.',
  },
  {
    key: 'subagents',
    pkg: 'subagent',
    title: 'Subagent provider registry',
    mode: 'seam',
    implementations: ['subagent-spawn', 'subagent-fork', 'subagent-acp', 'subagent-mock'],
    consumers: ['tool-subagent'],
    note: 'Providers implement transports; tool-subagent exposes one configured provider as a model-facing tool name.',
  },
  {
    key: 'web',
    pkg: 'web',
    title: 'Web access provider registry',
    mode: 'seam',
    implementations: ['web-search-exa', 'web-search-perplexity', 'web-search-deepseek', 'web-fetch-local'],
    consumers: ['tool-web'],
    note: 'Search and fetch providers register into one ctx.web seam; tool-web owns the stable model-facing names.',
  },
  {
    key: 'workflows',
    pkg: 'workflow',
    title: 'Workflow script engine',
    mode: 'seam',
    implementations: ['workflow-workerthread'],
    consumers: ['tool-workflow'],
    note: 'One engine per context (bash shape, no named-provider registry); the worker-thread engine fans agent() calls out through ctx.subagents.',
  },
]

const DYNAMIC_EVENT_DISPATCHERS: Array<{ event: string; pkg: string; method: string }> = [
  // Subagent lifecycle events intentionally bypass ctx.emit and call
  // ctx.events.dispatch directly so one throwing listener cannot starve later
  // listeners or strand an already-started child run.
  { event: 'subagent/start', pkg: 'subagent', method: 'events.dispatch' },
  { event: 'subagent/end', pkg: 'subagent', method: 'events.dispatch' },
  // The workflow/* lifecycle events dispatch the same way, for the same
  // per-listener-containment reason (WorkflowService.emitWorkflowEvent).
  { event: 'workflow/start', pkg: 'workflow', method: 'events.dispatch' },
  { event: 'workflow/phase', pkg: 'workflow', method: 'events.dispatch' },
  { event: 'workflow/log', pkg: 'workflow', method: 'events.dispatch' },
  { event: 'workflow/agent-start', pkg: 'workflow', method: 'events.dispatch' },
  { event: 'workflow/agent-end', pkg: 'workflow', method: 'events.dispatch' },
  { event: 'workflow/end', pkg: 'workflow', method: 'events.dispatch' },
]

function generatedHeader(title: string): string[] {
  return [
    '<!-- Generated by scripts/gen-doc-graphs.ts - do not edit by hand.',
    '     Run `pnpm run gen-doc-graphs` to regenerate. -->',
    '',
    `# ${title}`,
    '',
  ]
}

function maintenanceFooter(source: string): string[] {
  return [`Maintenance mode: ${source}.`, '']
}

function graphIndexLink(rel: string): string {
  return relative('docs', rel).replaceAll('\\', '/')
}

function linkFromDoc(docRel: string, targetRel: string): string {
  return relative(dirname(docRel), targetRel).replaceAll('\\', '/')
}

function collectPackages(): Pkg[] {
  const pkgs: Pkg[] = []
  for (const rel of globSync('packages/*/*/package.json', { cwd: root }).sort()) {
    const json = JSON.parse(readFileSync(resolve(root, rel), 'utf8')) as PkgJson
    if (!json.name.startsWith(SCOPE)) continue
    const [, group, leaf] = rel.split('/')
    if (group === undefined || leaf === undefined) throw new Error(`gen-doc-graphs: unexpected package path ${rel}`)
    const deps = Object.keys(json.peerDependencies ?? {})
      .filter(dep => dep.startsWith(SCOPE))
      .map(dep => dep.slice(SCOPE.length))
      .sort()
    pkgs.push({
      short: json.name.slice(SCOPE.length),
      name: json.name,
      group,
      rel: dirname(rel),
      deps,
    })
  }
  return topoSort(pkgs)
}

function topoSort(pkgs: Pkg[]): Pkg[] {
  const remaining = new Map(pkgs.map(p => [p.short, p]))
  const placed = new Set<string>()
  const out: Pkg[] = []
  while (remaining.size > 0) {
    const ready = [...remaining.values()]
      .filter(pkg => pkg.deps.every(dep => placed.has(dep)))
      .sort(comparePackages)
    if (ready.length === 0) throw new Error(`gen-doc-graphs: dependency cycle among ${[...remaining.keys()].join(', ')}`)
    for (const pkg of ready) {
      out.push(pkg)
      placed.add(pkg.short)
      remaining.delete(pkg.short)
    }
  }
  return out
}

function comparePackages(a: Pkg, b: Pkg): number {
  const groupA = GROUP_ORDER.indexOf(a.group)
  const groupB = GROUP_ORDER.indexOf(b.group)
  const normA = groupA === -1 ? Number.MAX_SAFE_INTEGER : groupA
  const normB = groupB === -1 ? Number.MAX_SAFE_INTEGER : groupB
  return normA - normB || a.group.localeCompare(b.group) || a.short.localeCompare(b.short)
}

function nodeId(prefix: string, value: string): string {
  return `${prefix}_${value.replace(/[^a-zA-Z0-9_]/g, '_')}`
}

function escLabel(value: string): string {
  return value.replace(/"/g, '\\"')
}

function mermaidCode(value: string): string {
  return `<code>${value.replace(/&/g, '&amp;').replace(/</g, '&lt;').replace(/>/g, '&gt;')}</code>`
}

function repoLink(path: string, label: string, up = '..'): string {
  return `[${label}](${up}/${path})`
}

function sourceLink(source: string, up = '..'): string {
  return repoLink(source.split(':')[0] ?? source, `\`${source}\``, up)
}

function pkgLink(pkg: Pkg | undefined, fallback: string, up = '..'): string {
  return pkg ? repoLink(pkg.rel, `\`${pkg.short}\``, up) : `\`${fallback}\``
}

function pkgList(names: string[] | undefined, pkgsByShort: Map<string, Pkg>): string {
  if (!names || names.length === 0) return '-'
  return names.map(name => pkgLink(pkgsByShort.get(name), name)).join(', ')
}

function tableCell(value: string): string {
  return value.replace(/\|/g, '\\|').replace(/\n/g, '<br>')
}

function assertServiceRolesComplete(): void {
  const discovered = new Set(collectServices().map(service => service.key))
  const classified = new Set(SERVICE_ROLES.map(role => role.key))
  const missing = [...discovered].filter(key => !classified.has(key)).sort()
  const stale = [...classified].filter(key => !discovered.has(key)).sort()
  if (missing.length || stale.length) {
    throw new Error([
      missing.length ? `missing service role classification: ${missing.join(', ')}` : '',
      stale.length ? `stale service role classification: ${stale.join(', ')}` : '',
    ].filter(Boolean).join('; '))
  }
}

function renderCapabilitySeams(pkgs: Pkg[]): string {
  assertServiceRolesComplete()
  const pkgsByShort = new Map(pkgs.map(pkg => [pkg.short, pkg]))
  const maintenance = 'hybrid: services are discovered from Cordis declarations; interface/implementation/consumer roles are classified in `scripts/gen-doc-graphs.ts` with a completeness guard'
  const nodes = new Map<string, string>()
  const edges = new Set<string>()
  const companionEdges = new Set<string>()
  const addNode = (id: string, label: string): void => {
    if (!nodes.has(id)) nodes.set(id, `  ${id}["${escLabel(label)}"]`)
  }
  const addEdge = (from: string, to: string): void => { edges.add(`  ${from} --> ${to}`) }
  const lines = generatedHeader('Capability Seams And Core Services')
  lines.push(
    'A service can be a core spine service, a swappable capability seam, or a bundle/composition point. The graph shows the package that owns the service declaration, known implementation packages, and packages that consume the service directly.',
    '',
    '```mermaid',
    'flowchart LR',
  )
  for (const role of SERVICE_ROLES) {
    const svc = nodeId('svc', role.key)
    const owner = nodeId('pkg', role.pkg)
    addNode(owner, role.pkg)
    addNode(svc, `ctx.${role.key}<br/>${role.title}`)
    addEdge(owner, svc)
    for (const impl of role.implementations ?? []) {
      addNode(nodeId('pkg', impl), impl)
      addEdge(nodeId('pkg', impl), svc)
    }
    for (const consumer of role.consumers ?? []) {
      addNode(nodeId('pkg', consumer), consumer)
      addEdge(svc, nodeId('pkg', consumer))
    }
    for (const companion of role.companions ?? []) {
      addNode(nodeId('pkg', companion), companion)
      companionEdges.add(`  ${svc} -. event gate .-> ${nodeId('pkg', companion)}`)
    }
  }
  lines.push(...nodes.values(), ...[...edges].sort(), ...[...companionEdges].sort())
  lines.push('```', '', '| ctx key | Role | Owner | Implementations | Direct consumers | Companion plugins | Note |', '| --- | --- | --- | --- | --- | --- | --- |')
  for (const role of SERVICE_ROLES) {
    lines.push(`| \`ctx.${role.key}\` | \`${role.mode}\` | ${pkgLink(pkgsByShort.get(role.pkg), role.pkg)} | ${pkgList(role.implementations, pkgsByShort)} | ${pkgList(role.consumers, pkgsByShort)} | ${pkgList(role.companions, pkgsByShort)} | ${tableCell(role.note)} |`)
  }
  lines.push('', ...maintenanceFooter(maintenance))
  return lines.join('\n')
}

function parseExampleCordis(rel: string): ExamplePlugin[] {
  const text = readFileSync(resolve(root, rel), 'utf8')
  const plugins: ExamplePlugin[] = []
  let current: { id: string; name?: string } | null = null
  const flush = (): void => {
    if (current?.name) plugins.push({ id: current.id, name: current.name })
  }
  for (const line of text.split('\n')) {
    const id = /^-\s+id:\s+(.+?)\s*$/.exec(line)
    if (id?.[1] !== undefined) {
      flush()
      current = { id: stripYamlScalar(id[1]) }
      continue
    }
    const name = /^\s+name:\s+(.+?)\s*$/.exec(line)
    if (name?.[1] !== undefined && current) current.name = stripYamlScalar(name[1])
  }
  flush()
  return plugins
}

function stripYamlScalar(value: string): string {
  return value.trim().replace(/^['"]|['"]$/g, '')
}

const APP_EXAMPLES = [
  {
    id: 'echo',
    rel: 'examples/echo-agent/composition.md',
    title: 'Echo Agent App Composition',
    label: 'examples/echo-agent',
    config: 'examples/echo-agent/cordis.yml',
    summary: 'The echo demo swaps in a local mock LLM and teaching echo tool, then loads the stdio app package for the shared spine and terminal front door.',
  },
  {
    id: 'coding',
    rel: 'examples/coding-agent/composition.md',
    title: 'Coding Agent App Composition',
    label: 'examples/coding-agent',
    config: 'examples/coding-agent/cordis.yml',
    summary: 'The coding REPL demo adds the real DeepSeek adapter, filesystem tools, todo_write, compaction, and both subagent transports on top of the stdio app package.',
  },
  {
    id: 'cordis',
    rel: 'examples/cordis-agent/composition.md',
    title: 'Cordis Agent App Composition',
    label: 'examples/cordis-agent',
    config: 'examples/cordis-agent/cordis.yml',
    summary: 'The self-referential demo puts @deepseek-ai/dsh-tool-cordis on the coding spine, letting the agent inspect its own runtime and mount/unmount plugins into it.',
  },
  {
    id: 'acp',
    rel: 'examples/acp-agent/composition.md',
    title: 'ACP Agent App Composition',
    label: 'examples/acp-agent',
    config: 'examples/acp-agent/cordis.yml',
    summary: 'The ACP demo exposes the same agent spine over JSON-RPC stdio, with no stdout logger and no pre-created agent; clients create sessions through the ACP bridge.',
  },
]

type AppExample = typeof APP_EXAMPLES[number]

function renderAppExpansion(lines: string[], appNode: string, pluginName: string): void {
  const agentCore = nodeId('bundle', 'agent_core')
  const jsonl = nodeId('bundle', 'jsonl')
  lines.push(`  ${appNode} --> ${agentCore}["@deepseek-ai/dsh-agent-core"]`)
  lines.push(`  ${appNode} --> ${jsonl}["@deepseek-ai/dsh-session-persistence-jsonl"]`)
  if (pluginName === '@deepseek-ai/dsh-stdio-agent') {
    lines.push(`  ${appNode} --> ${nodeId('frontdoor', 'stdio')}["readline UI<br/>console logger<br/>pre-created main agent"]`)
  } else if (pluginName === '@deepseek-ai/dsh-acp-agent') {
    lines.push(`  ${appNode} --> ${nodeId('frontdoor', 'acp')}["@deepseek-ai/dsh-acp<br/>JSON-RPC stdio bridge<br/>sessions created by client"]`)
  }
  lines.push(
    `  ${agentCore} --> ${nodeId('spine', 'llm')}["ctx.llm"]`,
    `  ${agentCore} --> ${nodeId('spine', 'sessions')}["ctx.sessions"]`,
    `  ${agentCore} --> ${nodeId('spine', 'tools')}["ctx.tools + tool-bash"]`,
    `  ${agentCore} --> ${nodeId('spine', 'loop')}["ctx.agents + ctx.agentLoop"]`,
  )
}

function renderAppComposition(example: AppExample): string {
  const plugins = parseExampleCordis(example.config)
  const maintenance = 'hybrid: the leaf plugin list is parsed from its `cordis.yml`; app package expansion is curated from package source'
  const lines = generatedHeader(example.title)
  lines.push(
    example.summary,
    '',
    '```mermaid',
    'flowchart LR',
    `  cfg["${escLabel(example.label)}<br/>cordis.yml"]`,
  )
  for (const plugin of plugins) {
    const pluginNode = nodeId(`plugin_${example.id}`, plugin.id)
    lines.push(`  ${pluginNode}["${escLabel(plugin.id)}<br/>${escLabel(plugin.name)}"]`)
    lines.push(`  cfg --> ${pluginNode}`)
    if (plugin.name === '@deepseek-ai/dsh-stdio-agent' || plugin.name === '@deepseek-ai/dsh-acp-agent') {
      renderAppExpansion(lines, pluginNode, plugin.name)
    }
  }
  lines.push(
    '```',
    '',
    '| Plugin id | Package / module |',
    '| --- | --- |',
    ...plugins.map(plugin => `| \`${plugin.id}\` | \`${plugin.name}\` |`),
    '',
    `Source config: [\`${example.config}\`](${linkFromDoc(example.rel, example.config)}).`,
  )
  lines.push('', ...maintenanceFooter(maintenance))
  return lines.join('\n')
}

function collectEventRelations(): Map<string, EventRelation> {
  const out = new Map<string, EventRelation>()
  const ensure = (event: string): EventRelation => {
    const existing = out.get(event)
    if (existing) return existing
    const next = { dispatchers: new Map<string, Set<string>>(), listeners: new Set<string>() }
    out.set(event, next)
    return next
  }
  for (const rel of globSync('packages/*/*/src/**/*.ts', { cwd: root }).sort()) {
    const [, , leaf] = rel.split('/')
    if (leaf === undefined) continue
    const text = readFileSync(resolve(root, rel), 'utf8')
    const sf = ts.createSourceFile(rel, text, ts.ScriptTarget.Latest, true)
    const visit = (node: ts.Node): void => {
      if (ts.isCallExpression(node) && ts.isPropertyAccessExpression(node.expression)) {
        const method = node.expression.name.text
        if (!isCordisContextReceiver(node.expression)) {
          ts.forEachChild(node, visit)
          return
        }
        if (method === 'on') {
          const event = eventArg(node.arguments, method)
          if (event) ensure(event).listeners.add(leaf)
        } else if (method === 'emit' || method === 'parallel' || method === 'serial' || method === 'waterfall') {
          const event = eventArg(node.arguments, method)
          if (event) {
            const relation = ensure(event)
            const methods = relation.dispatchers.get(leaf) ?? new Set<string>()
            methods.add(method)
            relation.dispatchers.set(leaf, methods)
          }
        }
      }
      ts.forEachChild(node, visit)
    }
    visit(sf)
  }
  for (const entry of DYNAMIC_EVENT_DISPATCHERS) {
    const relation = ensure(entry.event)
    const methods = relation.dispatchers.get(entry.pkg) ?? new Set<string>()
    methods.add(entry.method)
    relation.dispatchers.set(entry.pkg, methods)
  }
  return out
}

function isCordisContextReceiver(expr: ts.PropertyAccessExpression): boolean {
  const receiver = expr.expression
  if (ts.isIdentifier(receiver)) return receiver.text === 'ctx' || receiver.text === '_ctx'
  return ts.isPropertyAccessExpression(receiver)
    && receiver.expression.kind === ts.SyntaxKind.ThisKeyword
    && (receiver.name.text === 'ctx' || receiver.name.text === '_ctx')
}

function eventArg(args: ts.NodeArray<ts.Expression>, method: string): string | undefined {
  if (method === 'waterfall') {
    const arg = args.find(ts.isStringLiteralLike)
    return arg?.text
  }
  const first = args[0]
  return first && ts.isStringLiteralLike(first) ? first.text : undefined
}

function relationPackages(map: Map<string, Set<string>>, pkgsByShort: Map<string, Pkg>): string {
  if (map.size === 0) return '-'
  return [...map.entries()]
    .sort(([a], [b]) => a.localeCompare(b))
    .map(([pkg, methods]) => `${pkgLink(pkgsByShort.get(pkg), pkg)} (${[...methods].sort().map(m => `\`${m}\``).join(', ')})`)
    .join(', ')
}

function listenerPackages(listeners: Set<string>, pkgsByShort: Map<string, Pkg>): string {
  if (listeners.size === 0) return '-'
  return [...listeners].sort().map(pkg => pkgLink(pkgsByShort.get(pkg), pkg)).join(', ')
}

function renderEventRelations(pkgs: Pkg[]): string {
  const events = collectEvents()
  const relations = collectEventRelations()
  const pkgsByShort = new Map(pkgs.map(pkg => [pkg.short, pkg]))
  const maintenance = 'hybrid generated: Cordis event declarations and most producer/listener edges are AST-scanned; dynamic dispatch sites are classified in `scripts/gen-doc-graphs.ts`'
  const lines = generatedHeader('Event Producer And Consumer Matrix')
  lines.push(
    'This matrix shows which packages dispatch each harness-owned event and which packages listen to it. It is intentionally a table rather than one large graph: events are many-to-many, and dense relation data is easier to review in rows. Dynamic dispatch overrides cover sites that deliberately bypass `ctx.emit`, such as subagent lifecycle containment.',
    '',
    '| Event | Mode | Declared in | Dispatchers | Listeners |',
    '| --- | --- | --- | --- | --- |',
  )
  for (const event of [...events].sort((a, b) => a.name.localeCompare(b.name))) {
    const relation = relations.get(event.name) ?? { dispatchers: new Map<string, Set<string>>(), listeners: new Set<string>() }
    lines.push(`| \`${event.name}\` | \`${event.mode}\` | ${sourceLink(event.source)} | ${relationPackages(relation.dispatchers, pkgsByShort)} | ${listenerPackages(relation.listeners, pkgsByShort)} |`)
  }
  const declared = new Set(events.map(event => event.name))
  const extra = [...relations.keys()].filter(event => !declared.has(event)).sort()
  if (extra.length > 0) {
    lines.push('', '## Non-harness or undeclared event strings seen in package source', '', '| Event string | Dispatchers | Listeners |', '| --- | --- | --- |')
    for (const event of extra) {
      const relation = relations.get(event)
      if (!relation) continue
      lines.push(`| \`${event}\` | ${relationPackages(relation.dispatchers, pkgsByShort)} | ${listenerPackages(relation.listeners, pkgsByShort)} |`)
    }
  }
  lines.push('', ...maintenanceFooter(maintenance))
  return lines.join('\n')
}

function renderLifecycle(): string {
  const maintenance = 'curated Mermaid sequence; exact event signatures live in the generated Cordis catalog'
  return [
    ...generatedHeader('Agent Turn And Step Lifecycle'),
    'This sequence is the visual companion to [architecture.md](architecture.md#loop-lifecycle-session--turn--step). It keeps durable replay facts on `session/event` and live control/status on `agent/*`.',
    '',
    '```mermaid',
    'sequenceDiagram',
    '  participant User',
    '  participant Agent',
    '  participant Driver',
    '  participant Hooks as hook listeners',
    '  participant Prompt as ctx.systemPrompt',
    '  participant LLM as ctx.llm',
    '  participant Tools as ctx.tools',
    '  participant Session',
    '  participant Persistence',
    '  participant SDK as UI or SDK listener',
    '  User->>Agent: send(content)',
    `  Agent-->>SDK: ${mermaidCode('agent/queued')}`,
    '  Agent->>Driver: queued work wakes driver',
    `  Driver-->>SDK: ${mermaidCode('agent/status')} running`,
    `  Driver->>Session: ${mermaidCode('turn/start')}`,
    `  Driver->>Hooks: ${mermaidCode('agent/prompt-submit')} waterfall`,
    '  Hooks-->>Driver: allow, block, or add context',
    `  Driver->>Session: ${mermaidCode('user/message')} or rejected ${mermaidCode('turn/end')}`,
    `  Driver->>Prompt: ${mermaidCode('system-prompt/assemble')} waterfall`,
    `  Driver-->>Driver: ${mermaidCode('agent/pre-step')} serial checkpoint`,
    `  Driver->>Session: ${mermaidCode('step/start')}`,
    `  Driver->>LLM: ${mermaidCode('agent/request')} waterfall, then ${mermaidCode('llm/stream')} waterfall`,
    '  LLM-->>Driver: StreamChunk*',
    `  Driver->>Session: ${mermaidCode('assistant/chunk')}*`,
    `  Session-->>SDK: ${mermaidCode('session/event')} ${mermaidCode('assistant/chunk')}*`,
    `  Driver->>Hooks: ${mermaidCode('agent/step-result')} waterfall`,
    `  Driver->>Session: ${mermaidCode('assistant/message')}`,
    `  Driver->>Session: ${mermaidCode('tool/call')}`,
    '  Driver->>Tools: execute through pre and post waterfalls',
    '  Tools-->>Session: tool-owned events when applicable',
    `  Driver->>Session: ${mermaidCode('tool/result')} and ${mermaidCode('step/end')}`,
    `  Driver->>Hooks: ${mermaidCode('agent/turn-continuation')} waterfall`,
    `  Driver->>Session: ${mermaidCode('turn/end')}`,
    `  Driver->>Persistence: ${mermaidCode('session/flush')} parallel checkpoint`,
    `  Driver-->>SDK: ${mermaidCode('agent/status')} idle`,
    '```',
    '',
    'SDK users that need replayable transcript data should consume `session/event`; `agent/*` is the live coordination surface for queue/status, prompt interception, request shaping, steering, continuation, and errors.',
    '',
    ...maintenanceFooter(maintenance),
  ].join('\n')
}

function renderToolPipeline(): string {
  const maintenance = 'curated Mermaid flow; exact tool schemas and event signatures live in generated catalogs'
  return [
    ...generatedHeader('Tool Execution Pipeline'),
    'This graph shows where policy, hooks, sandboxing, filesystem guards, result rewriting, and UI rendering fit without changing the loop. The key extension points are the `tools/pre-execute`, `tools/execute`, and `tools/post-execute` waterfalls.',
    '',
    '```mermaid',
    'flowchart TD',
    '  model["Assistant message contains tool-call block"]',
    `  toolCall["Session event: ${mermaidCode('tool/call')}<br/>logged before execution"]`,
    '  presentCall["UI pending card<br/>presentCall(args)"]',
    `  pre["${mermaidCode('tools/pre-execute')} waterfall<br/>hooks, permission, sandbox"]`,
    '  denied["deny or ask<br/>tool body skipped"]',
    `  around["${mermaidCode('tools/execute')} waterfall<br/>timeout, retry, metrics (around dispatch)"]`,
    '  toolBody["Registered tool execute() body"]',
    `  fsGate["${mermaidCode('fs/write-intent')} or ${mermaidCode('fs/edit-intent')}<br/>tool-fs mutations only"]`,
    `  owned["Tool-owned session events<br/>${mermaidCode('todo/write')}, ${mermaidCode('fs/observed')}, ${mermaidCode('hook/invoked')}, ${mermaidCode('hook/result')}, ${mermaidCode('tool/code-dispatch')}"]`,
    `  post["${mermaidCode('tools/post-execute')} waterfall<br/>accept, block, replace, add context"]`,
    '  context["Buffered additionalContext<br/>context/message after all tool results"]',
    `  toolResult["Session event: ${mermaidCode('tool/result')}<br/>single model-facing outcome"]`,
    '  presentResult["UI completed card<br/>presentResult(args, result)"]',
    '  model --> toolCall',
    '  toolCall --> presentCall',
    '  toolCall --> pre',
    '  pre -->|allow| around',
    '  around --> toolBody',
    '  pre -->|deny or ask| denied',
    '  denied --> post',
    '  toolBody --> fsGate',
    '  fsGate --> toolBody',
    '  toolBody --> owned',
    '  toolBody --> around',
    '  around --> post',
    '  post --> context',
    '  post --> toolResult',
    '  toolResult --> presentResult',
    '```',
    '',
    'Filesystem read-before-edit checks live below `tool-fs` on the `fs/*` event gate; hook bridges and future permission prompts live on the generic pre/post tool waterfalls; and around-dispatch concerns like the tool-call timeout policy (`@deepseek-ai/dsh-timeout-policy`) wrap core dispatch on `tools/execute`. That split lets the same hooks observe bash, fs, web, todo, and subagent calls without coupling those tools to one policy service. Code Mode rides the same pipeline twice over: `run_code` is itself a registered tool body, and each tool call its program makes re-enters `ctx.tools.execute()` through BOTH waterfalls — serialized one at a time, logged as a `tool/code-dispatch` session event, with a deny surfacing to the program as a binding rejection (a sub-call\'s `additionalContext` is deliberately dropped — no safe outlet mid-run preserves call/result adjacency).',
    '',
    ...maintenanceFooter(maintenance),
  ].join('\n')
}

function renderSnapshotReplay(): string {
  const maintenance = 'curated Mermaid sequence based on the snapshot test harness'
  return [
    ...generatedHeader('ACP Snapshot Replay'),
    'This graph explains what a snapshot scenario proves: recorded real-model session logs are replayed keylessly, ACP stdout is normalized and diffed, and scenario workspaces preserve tool side effects that the UI stream alone cannot prove.',
    '',
    '```mermaid',
    'sequenceDiagram',
    '  participant Recorder as Real API recording',
    '  participant Fixture as snapshot fixture',
    '  participant Workspace',
    '  participant Replay as llm-replay adapter',
    '  participant ACP as acp-agent subprocess',
    '  participant Golden as stdout golden',
    '  Recorder->>Fixture: session.jsonl + workspace inputs',
    '  Fixture->>Workspace: seed files and hook configs',
    '  Fixture->>Replay: recorded StreamChunk script',
    `  Replay->>ACP: deterministic ${mermaidCode('llm/stream')} chunks`,
    '  ACP->>Workspace: bash, fs, and hook side effects',
    '  ACP->>Golden: normalized sessionUpdate stream',
    '  Golden-->>ACP: diff must be empty',
    '```',
    '',
    'The fs and hook snapshot matrix is valuable because it proves world state, hook decisions, and failed tool-card rendering, not just that replay returns text.',
    '',
    ...maintenanceFooter(maintenance),
  ].join('\n')
}

function renderDocs(): GraphDoc[] {
  const pkgs = collectPackages()
  const docs: GraphDoc[] = [
    { rel: 'docs/capability-seams.md', content: renderCapabilitySeams(pkgs) },
    ...APP_EXAMPLES.map(example => ({ rel: example.rel, content: renderAppComposition(example) })),
    { rel: 'docs/event-producer-consumer.md', content: renderEventRelations(pkgs) },
    { rel: 'docs/agent-lifecycle.md', content: renderLifecycle() },
    { rel: 'docs/tool-execution-pipeline.md', content: renderToolPipeline() },
    { rel: 'packages/ui/acp/snapshot-replay.md', content: renderSnapshotReplay() },
  ]
  docs.unshift({ rel: 'docs/graph-atlas.md', content: renderIndex(docs) })
  return docs
}

function renderIndex(docs: GraphDoc[]): string {
  const labels: Record<string, string> = {
    'docs/capability-seams.md': 'capability seams and core services',
    'examples/echo-agent/composition.md': 'echo-agent app composition',
    'examples/coding-agent/composition.md': 'coding-agent app composition',
    'examples/cordis-agent/composition.md': 'cordis-agent app composition',
    'examples/acp-agent/composition.md': 'acp-agent app composition',
    'docs/event-producer-consumer.md': 'event producer/consumer matrix',
    'docs/agent-lifecycle.md': 'agent turn and step lifecycle',
    'docs/tool-execution-pipeline.md': 'tool execution pipeline',
    'packages/ui/acp/snapshot-replay.md': 'ACP snapshot replay',
  }
  const modes: Record<string, string> = {
    'docs/capability-seams.md': 'hybrid generated',
    'examples/echo-agent/composition.md': 'hybrid generated',
    'examples/coding-agent/composition.md': 'hybrid generated',
    'examples/cordis-agent/composition.md': 'hybrid generated',
    'examples/acp-agent/composition.md': 'hybrid generated',
    'docs/event-producer-consumer.md': 'hybrid generated',
    'docs/agent-lifecycle.md': 'curated',
    'docs/tool-execution-pipeline.md': 'curated',
    'packages/ui/acp/snapshot-replay.md': 'curated',
  }
  const rows = [
    '| [module dependency graph](module-graph.md) | `generated` |',
    '| [tool schema catalog and package map](tool-catalog.md) | `generated` |',
    ...docs.map((doc) => {
      const link = graphIndexLink(doc.rel)
      return `| [${labels[doc.rel] ?? link}](${link}) | \`${modes[doc.rel] ?? 'generated'}\` |`
    }),
  ]
  const maintenance = 'mixed: each linked page declares generated, hybrid, or curated mode'
  return [
    ...generatedHeader('Documentation Graph Index'),
    'These diagrams are the relationship layer above the generated catalogs. Use them to navigate package topology, capability seams, event flow, model-facing tools, app composition, and runtime lifecycle paths. Exact signatures and type shapes still live in the generated [events](cordis-catalog/events.md) / [services](cordis-catalog/services.md) catalogs, [tool-catalog.md](tool-catalog.md), and [core-data-structures/](core-data-structures/core.md).',
    '',
    'The process decision behind this index is recorded in [the documentation graph RFC](rfc/implemented/process/2026-07-03-documentation-graph-atlas.md).',
    '',
    '| Graph | Mode |',
    '| --- | --- |',
    ...rows,
    '',
    'Regenerate with `pnpm run gen-doc-graphs`; verify freshness with `pnpm run verify-doc-graphs`.',
    '',
    ...maintenanceFooter(maintenance),
  ].join('\n')
}

function main(): void {
  const docs = renderDocs()
  if (process.argv.includes('--check')) {
    const stale: string[] = []
    for (const doc of docs) {
      const abs = resolve(root, doc.rel)
      const committed = existsSync(abs) ? readFileSync(abs, 'utf8') : null
      if (committed !== doc.content) stale.push(doc.rel)
    }
    if (stale.length === 0) {
      console.log(`gen-doc-graphs: ${docs.length} graph doc(s) are up to date.`)
      return
    }
    console.error(`gen-doc-graphs: stale graph doc(s): ${stale.join(', ')}. Run \`pnpm run gen-doc-graphs\` and commit the result.`)
    process.exit(1)
  }

  for (const doc of docs) {
    mkdirSync(dirname(resolve(root, doc.rel)), { recursive: true })
    writeFileSync(resolve(root, doc.rel), doc.content)
  }
  console.log(`gen-doc-graphs: wrote ${docs.length} graph doc(s).`)
}

if (process.argv[1] && import.meta.filename === resolve(process.argv[1])) {
  main()
}