docs(x): fix pointers the reorg docs pass got wrong or missed

The Phase B docs pass introduced two errors in VIDEO_MODE.md's prompt
catalog (composer still at the pre-move agents/ path; frame-context
pointed at legacy/engine.ts when convertFromMessages lives in
runtime/assembly/message-encoding.ts) and missed ANALYTICS.md entirely
(copilot_chat emit point still cited agents/runtime.ts:1313, file_parse
still cited the deleted builtin-tools.ts monolith).
turn-runtime-design.md referenced the repo-root AGENTS.md, which is not
committed — the carve-out is now stated inline. Also drops a leftover
debug comment in skills/index.ts.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

apps/x/ANALYTICS.md

@@ -41,9 +41,9 @@ Every `llm_usage` emit point in the codebase:
 
 | `use_case` | `sub_use_case` | `agent_name`? | Where | File:line |
 |---|---|---|---|---|
-| `copilot_chat` | (none) | yes | User chat in renderer (default for any `createRun` without `useCase`) | `packages/core/src/agents/runtime.ts:1313` (finish-step in `streamLlm`) |
+| `copilot_chat` | (none) | yes | User chat in renderer (turn runtime; the ALS default when no caller set a use case) | `packages/core/src/runtime/turns/bridges/real-usage-reporter.ts` (`reportModelUsage`); legacy runs (code-mode carve-out) still emit from `packages/core/src/runtime/legacy/engine.ts` (`streamLlm` finish-step) |
 | `copilot_chat` | `scheduled` | yes | Background scheduled agent runner | `packages/core/src/agent-schedule/runner.ts:167` |
-| `copilot_chat` | `file_parse` | inherits | `parseFile` builtin tool inside any chat | `packages/core/src/application/lib/builtin-tools.ts:770` |
+| `copilot_chat` | `file_parse` | inherits | `parseFile` builtin tool inside any chat | `packages/core/src/runtime/tools/domains/parsing.ts:179` |
 | `live_note_agent` | `routing` | no | Pass 1 routing classifier (`generateObject`) | `packages/core/src/knowledge/live-note/routing.ts:93` |
 | `live_note_agent` | `manual` | yes | Pass 2 agent run — user clicked Run / called the `run-live-note-agent` tool | `packages/core/src/knowledge/live-note/runner.ts:140` (createRun, `subUseCase: trigger`) |
 | `live_note_agent` | `cron` | yes | Pass 2 agent run — cron expression matched | same call site |

apps/x/VIDEO_MODE.md

@@ -176,10 +176,10 @@ Push-to-talk is disabled while a call owns the mic.
 
 | Prompt | Where |
 |--------|-------|
-| `# Video Mode (Live Camera)` system section — how to use webcam frames, coaching guidance, screen-share rules ("treat the screen as the primary subject", "last screen frame is current"), etiquette (never comment on appearance) | `packages/core/src/runtime/assembly/capabilities/modes.ts` (the `VIDEO_MODE` fragment of the `video-mode` capability, composed by `agents/compose-instructions.ts`) |
+| `# Video Mode (Live Camera)` system section — how to use webcam frames, coaching guidance, screen-share rules ("treat the screen as the primary subject", "last screen frame is current"), etiquette (never comment on appearance) | `packages/core/src/runtime/assembly/capabilities/modes.ts` (the `VIDEO_MODE` fragment of the `video-mode` capability, composed by `runtime/assembly/compose-instructions.ts`) |
 | `# Practice Session (Coach Mode)` system section — coaching persona: specific/actionable feedback after each take, one-sentence interjections mid-flow, structured debrief on wrap-up | `capabilities/modes.ts` (the `COACH_MODE` fragment, directly after the video capability) |
 | "Driving the app" paragraph in the video-mode section — on calls, prefer app-navigation read-view/open-item (show while telling) over describing or squinting at frames | same `# Video Mode` section; full action docs in the `app-navigation` skill (`runtime/assembly/skills/app-navigation/skill.ts`) |
-| Per-message frame context line `[Video mode: N live webcam frames … and M frames of the user's shared screen …]` + group labels | `packages/core/src/runtime/legacy/engine.ts` (`convertFromMessages`) |
+| Per-message frame context line `[Video mode: N live webcam frames … and M frames of the user's shared screen …]` + group labels | `packages/core/src/runtime/assembly/message-encoding.ts` (`convertFromMessages`) |
 | `videoMode` / `coachMode` composition overrides (session-sticky; flips bust prefix cache) | `packages/core/src/runtime/turns/bridges/real-agent-resolver.ts` (`CompositionOverrides`); set from `App.tsx` `sendConfig` |
 
 Voice input/output prompt sections (`# Voice Input`, `# Voice Output`) are

apps/x/packages/core/docs/turn-runtime-design.md

@@ -1,9 +1,10 @@
 # Turn Runtime Technical Specification
 
 Status: implemented and live. All chat, background, and knowledge callers
-run on this runtime; the legacy runs runtime remains only for code-mode
-sessions (see the carve-out section in the repo-root `AGENTS.md`). The
-companion session layer is specified in `session-design.md`.
+run on this runtime; the legacy runs runtime (`src/runtime/legacy/`) remains
+only for code-mode sessions and the mini-apps host API, and is deleted as a
+unit when those migrate. The companion session layer is specified in
+`session-design.md`.
 
 This document specifies a new turn-oriented agent loop for `@x/core`. It is
 intended to replace the behavioral responsibilities of the current run runtime

apps/x/packages/core/src/runtime/assembly/skills/index.ts

@@ -36,8 +36,6 @@ const CATALOG_PREFIX = "src/runtime/assembly/skills";
 // carry loadSkill references under this prefix, so it stays a resolvable alias.
 const LEGACY_CATALOG_PREFIX = "src/application/assistant/skills";
 
-// console.log(liveNoteSkill);
-
 // A skill IS the model-activated variant of the capability record
 // (capabilities/types.ts): lazy guidance the model pulls in via loadSkill,
 // plus the BuiltinTools it owns. `id` doubles as the folder name. Tool names