refactor(cli)!: one shared base config with per-surface overlays

`dsh` shipped two config trees that were 43 rows the same: apps/cli/cordis.yml
composed web as 74 flat rows, while the TUI booted examples/tui-agent/cordis.yml
whose single `@deepseek-ai/dsh-tui-demo` row mounted twelve plugins behind a
twenty-key pass-through Config. Neither file was what its location claimed —
apps/cli hardcoded the "example" as the product default and the "demo" bundle
was the application — and every capability change had to be made twice.

- apps/cli/base.cordis.yml holds the 43 shared rows; tui.cordis.yml and
  web.cordis.yml are patch lists stating only what differs per surface
- overlays apply as SIBLING patch lists at one include level, because include
  patches never cross an include boundary. Precedence: base < surface <
  (--config | personal ~/.dsh/config.yaml) < launcher flag/profile patches
- `--config` now applies an overlay INSTEAD OF the personal one, so a demo or
  test tree never inherits the user's route; new `--config-replace` boots a file
  as the entire tree (the old `--config` behaviour). Both survive /resume
- vendor/include: index each `insert`ed row as it is added so a later patch can
  configure or disable it. Upstream built the id index once before the patch
  loop, leaving every surface-only row — the whole TUI front door — silently
  unpatchable from user config. Logged as local modification 8
- session identity moves to dsh-agent-loop's CONFIGURED_AGENT_IDENTITIES_KEY;
  dsh-tui's MAIN_SESSION_ID_KEY is deleted (only the bundle read it)
- delete examples/tui-agent, examples/cordis-agent, packages/examples/tui-demo;
  TUI tests → apps/cli/tests, cordis e2e → packages/cordis/tool-cordis/tests,
  examples/code-mode survives as an overlay leaf
- `dsh web` gains --config, threaded into AppCLIEntry as an extra overlay

Three latent defects surfaced and are fixed here: the TUI captured the optional
sessionQuery service once at construction and could permanently disable /resume
when it won the mount race; the session-store root silently reverted to a
project-local ./.sessions; --config-replace was dropped by the resume handoff.

Verified by booting each tree through the real Loader (TUI 55 entries, web 75,
zero unsettled) rather than reading YAML. All eight terminal snapshots replay
byte-identically; 14/14 PTY smoke, 112/112 snapshots, 25/25 doc-sync, hygiene
and lint clean.

scripts/demo-code-mode.mjs

@@ -12,7 +12,7 @@ const UIS = new Map([
     'tsx/esm',
     'apps/cli/src/bin.ts',
     '--config',
-    'examples/tui-agent/code-mode.cordis.yml',
+    'examples/code-mode/cordis.yml',
   ]],
   ['acp', ['--import', 'tsx', 'packages/examples/acp-demo/src/bin.ts', '--config', 'examples/acp-agent/code-mode.cordis.yml']],
 ])

scripts/demo-cordis.mjs

@@ -1,21 +1,19 @@
 /**
- * Boot the self-referential Cordis tools under TUI, Web, or ACP, defaulting
- * to TUI. This is a repository demo wrapper, not a product CLI feature.
+ * Boot the self-referential Cordis tools under Web or ACP, defaulting to Web. This is a repository demo wrapper, not a product CLI feature.
  */
 import { spawn } from 'node:child_process'
 
 const SURFACES = new Map([
-  ['tui', ['--import', 'tsx', 'apps/cli/src/bin.ts', '--config', 'examples/cordis-agent/cordis.yml']],
-  // `dsh web` does not accept alternate configs yet. The TUI config escape
-  // hatch still boots this browser-only tree; the config owns port 3081.
-  ['web', ['--import', 'tsx', 'apps/cli/src/bin.ts', '--config', 'examples/web-cordis/cordis.yml']],
+  // The browser surface with the cordis toolset layered on: `dsh web --config`
+  // applies this overlay over the shipped web composition; it owns port 3081.
+  ['web', ['--import', 'tsx', 'apps/cli/src/bin.ts', 'web', '--config', 'examples/web-cordis/cordis.yml']],
   ['acp', ['--import', 'tsx', 'packages/examples/acp-demo/src/bin.ts', '--config', 'examples/acp-agent/cordis-tools.cordis.yml']],
 ])
 
-const surface = process.argv[2] ?? 'tui'
+const surface = process.argv[2] ?? 'web'
 const args = SURFACES.get(surface)
 if (args === undefined || process.argv.length > 3) {
-  console.error('usage: pnpm run demo:cordis [tui|web|acp]')
+  console.error('usage: pnpm run demo:cordis [web|acp]')
   process.exit(2)
 }
 

scripts/gen-doc-graphs.ts

@@ -282,7 +282,7 @@ const SERVICE_ROLES: ServiceRole[] = [
     pkg: 'agent',
     title: 'Agent service',
     mode: 'core',
-    consumers: ['agent-loop', 'acp', 'cli-demo', 'subagent-inprocess', 'tui-demo'],
+    consumers: ['agent-loop', 'acp', 'cli-demo', 'subagent-inprocess'],
     note: 'Owns live Agent handles, the create/resume factory seam, and process-local initiator propagation.',
   },
   {
@@ -603,10 +603,10 @@ function stripYamlScalar(value: string): string {
 const APP_EXAMPLES = [
   {
     id: 'tui',
-    rel: 'examples/tui-agent/composition.md',
-    title: 'TUI Agent App Composition',
-    label: 'examples/tui-agent',
-    config: 'examples/tui-agent/cordis.yml',
+    rel: 'apps/cli/composition.md',
+    title: 'dsh TUI Composition',
+    label: 'apps/cli (dsh)',
+    config: 'apps/cli/base.cordis.yml',
     summary: 'The TUI agent combines the real DeepSeek adapter, coding tools, compaction, subagents, and workflows with the full-screen terminal app package.',
   },
   {
@@ -617,14 +617,6 @@ const APP_EXAMPLES = [
     config: 'examples/headless-agent/cordis.yml',
     summary: 'The headless demo combines the real DeepSeek adapter and coding capabilities with the one-shot app package, format-pure stdout, and one fresh persisted top-level session.',
   },
-  {
-    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 current-process runtime and mount or unmount in-memory temporary Plugins.',
-  },
   {
     id: 'acp',
     rel: 'examples/acp-agent/composition.md',
@@ -642,9 +634,7 @@ function renderAppExpansion(lines: string[], appNode: string, pluginName: string
   const jsonl = nodeId('bundle', 'jsonl')
   lines.push(`  ${appNode} --> ${agentCore}["@deepseek-ai/dsh-agent-spine-demo"]`)
   lines.push(`  ${appNode} --> ${jsonl}["@deepseek-ai/dsh-session-persistence-jsonl"]`)
-  if (pluginName === '@deepseek-ai/dsh-tui-demo') {
-    lines.push(`  ${appNode} --> ${nodeId('frontdoor', 'tui')}["@deepseek-ai/dsh-tui<br/>pre-created main agent"]`)
-  } else if (pluginName === '@deepseek-ai/dsh-cli-demo') {
+  if (pluginName === '@deepseek-ai/dsh-cli-demo') {
     lines.push(`  ${appNode} --> ${nodeId('frontdoor', 'cli')}["one-shot driver<br/>format-pure stdout<br/>fresh top-level agent"]`)
   } else if (pluginName === '@deepseek-ai/dsh-acp-demo') {
     lines.push(`  ${appNode} --> ${nodeId('frontdoor', 'acp')}["@deepseek-ai/dsh-acp<br/>automation-only JSON-RPC stdio<br/>fresh sessions created by client"]`)
@@ -672,7 +662,7 @@ function renderAppComposition(example: AppExample): string {
     const pluginNode = nodeId(`plugin_${example.id}`, plugin.id)
     lines.push(`  ${pluginNode}["${escLabel(plugin.id)}<br/>${escLabel(plugin.name)}"]`)
     lines.push(`  cfg --> ${pluginNode}`)
-    if (plugin.name === '@deepseek-ai/dsh-tui-demo' || plugin.name === '@deepseek-ai/dsh-cli-demo' || plugin.name === '@deepseek-ai/dsh-acp-demo') {
+    if (plugin.name === '@deepseek-ai/dsh-cli-demo' || plugin.name === '@deepseek-ai/dsh-acp-demo') {
       renderAppExpansion(lines, pluginNode, plugin.name)
     }
   }
@@ -1184,8 +1174,7 @@ function renderIndex(docs: GraphDoc[]): string {
   const labels: Record<string, string> = {
     'docs/capability-seams.md': 'capability seams and core services',
     'examples/headless-agent/composition.md': 'headless-agent app composition',
-    'examples/tui-agent/composition.md': 'tui-agent app composition',
-    'examples/cordis-agent/composition.md': 'cordis-agent app composition',
+    'apps/cli/composition.md': 'dsh TUI 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',
@@ -1194,8 +1183,7 @@ function renderIndex(docs: GraphDoc[]): string {
   const modes: Record<string, string> = {
     'docs/capability-seams.md': 'hybrid generated',
     'examples/headless-agent/composition.md': 'hybrid generated',
-    'examples/tui-agent/composition.md': 'hybrid generated',
-    'examples/cordis-agent/composition.md': 'hybrid generated',
+    'apps/cli/composition.md': 'hybrid generated',
     'examples/acp-agent/composition.md': 'hybrid generated',
     'docs/event-producer-consumer.md': 'hybrid generated',
     'docs/agent-lifecycle.md': 'curated',

scripts/gen-tool-catalog.ts

@@ -215,7 +215,7 @@ const TOOL_PACKAGES: ToolPackage[] = [
       await ctx.plugin(ToolCordis)
     },
     note:
-      'Ships in examples/cordis-agent only (a deliberate opt-in — temporary Plugin code reaches the real runtime, see .agents/notes/implemented/feature/2026-07-08-self-referential-cordis-toolset.md). Plugins created by cordis_mount may register ADDITIONAL model-visible tools until unmounted or DSH restarts; a full changed request header logs those tool-set changes.',
+      'Not in any shipped tree (a deliberate opt-in — temporary Plugin code reaches the real runtime, see .agents/notes/implemented/feature/2026-07-08-self-referential-cordis-toolset.md). Plugins created by cordis_mount may register ADDITIONAL model-visible tools until unmounted or DSH restarts; a full changed request header logs those tool-set changes.',
   },
   {
     pkg: '@deepseek-ai/dsh-tool-fs',
@@ -348,7 +348,7 @@ const TOOL_PACKAGES: ToolPackage[] = [
       await ctx.plugin(ToolSubagent, { provider: 'mock' })
     },
     note:
-      'The registered tool name is the load-time `toolName` config (default `subagent`); the schema above is that default. The shipped example agents load this package once per subagent backend, so the model additionally sees `subagent_fork` (bound to the fork backend) with an identical schema — see `examples/tui-agent/cordis.yml` and `examples/acp-agent/cordis.yml`.',
+      'The registered tool name is the load-time `toolName` config (default `subagent`); the schema above is that default. The shipped example agents load this package once per subagent backend, so the model additionally sees `subagent_fork` (bound to the fork backend) with an identical schema — see `apps/cli/base.cordis.yml` and `examples/acp-agent/cordis.yml`.',
   },
   {
     pkg: '@deepseek-ai/dsh-tool-tasks',

scripts/run-gates.ts

@@ -526,7 +526,7 @@ function builtBinSmokeGate(needs: string[] = ['build']): Gate {
     '--config',
     'vitest.e2e.config.ts',
     'examples/headless-agent/tests/keyless-smoke.e2e.ts',
-    'examples/tui-agent/tests/tui-keyless-smoke.e2e.ts',
+    'apps/cli/tests/tui-keyless-smoke.e2e.ts',
     'packages/examples/cli-demo/tests/built-bin.e2e.ts',
     'packages/examples/acp-demo/tests/built-bin.e2e.ts',
     'packages/ui/jsonrpc/tests/built-scope-carrier.e2e.ts',

scripts/verify-cordis-config.ts

@@ -124,7 +124,7 @@ function validateExampleResolution(): string[] {
 
 function validateAppResolution(): string[] {
   const dependencies = readManifest('apps/cli/package.json').dependencies ?? {}
-  const references = pluginReferences.filter(reference => reference.file === 'apps/cli/cordis.yml')
+  const references = pluginReferences.filter(reference => reference.file === 'apps/cli/base.cordis.yml')
   return missingPluginDependencies(references, dependencies, 'apps/cli/package.json')
 }