phase: 158_thinking_timeline

All verification complete. Every gate is green and the docs check out. Final report:

## Phase 158 final verification pass — COMPLETE

**Verified (all tasks pre-completed; this pass re-ran the full gate):**
- Unit + integration: `uv run pytest --cov=app --cov-report=term-missing` → **3618 passed, 99% coverage on `app/`** (>90% gate)
- Phase E2E in isolation: `uv run pytest tests/e2e/test_thinking_timeline.py -v --no-cov` → **6/6 passed** (order pin, fold-at-rest, live-open, restore+`segments` array, shared page, no-thinking single disclosure)
- Regression E2E, each in isolation: `test_thinking_display` 5✓, `test_tool_call_compact` 4✓, `test_turn_progress_loader` 3✓ (per-run pin updated), `test_big_read_progress` 4✓, `test_agent_document_tools` 4✓, `test_share_chat` 4✓, `test_chat_persistence` 4✓, `test_smoke` 3✓
- Lint/types: `uv run ruff check . && uv run pyright` → **clean (0 errors)**

**Completion criteria:** all 9 met — timeline E2E pins ✓, restore/shared `segments` ✓, no-thinking single-disclosure + the three UNCHANGED regression suites green ✓, pre-phase byte-identical round-trip (integration pin: key absent, never null; >50 / >32 000 / empty text / unknown kind all 422) ✓, full suite + coverage + E2E + lint ✓, `git diff --stat` footprint limited to `app/schemas.py`, `frontend/assets/{app,shared}.js`, `tests/`, README, phase files (a pre-existing owner `TODO.md` edit is out of scope, not staged by the phase commit) ✓, D15→per-run supersession recorded in the updated pin ✓. (Commit + phase move are the harness's job; task dirs already in `complete/`.)

**Documentation:** README.md — Thinking section correctly describes the phase-158 timeline; config reference matches `.env.example` exactly; page table matches registered routes; no stale single-block wording. AGENTS.md — rules and quick-reference commands all accurate. **Verified consistent — no changes needed.**

**Decisions/deviations:** none. `test_tool_call_compact.py` carries a one-line docstring-only update (referenced the removed `closeToolCalls`); its test logic is byte-identical to the phase-117 contract and green.

**Next pending phase:** none — `todo/` contains only 158.

.agents/phases/complete/158_thinking_timeline/00_phase.md

@@ -0,0 +1,427 @@
+# Phase 158 — Chronological thinking / tool-call timeline
+
+**Source:** owner report (live interactive-browser session, 2026-10-04, shared page
+`https://brain.reeseapps.com/shared/95dd7a2a-8cda-478b-b694-53936070b9fb` — a real
+`turbo` turn with 6 tool calls): "the thinking block happens first but LLM sent a
+normal response, not a thinking response, and then went back to thinking. This is
+awkward. Then the tool calling happens, and the thinking block reads strangely
+because the tool calls are shown below the thinking block. … show the thinking /
+tool call / responses in order, rather than in single big blocks each."
+**Story:** n/a (owner bug report — live site, 2026-10-04)
+**Context:** `app/rag/agent.py::run_agent` (yields `thinking` / `content` /
+`ToolCallPiece` / `ToolResultPiece` in TRUE chronological order per round —
+thinking → tool call → thinking → … → answer; the SSE mapping in
+`app/api/chat.py` preserves that order, so NO backend stream change is needed);
+`frontend/assets/app.js` — `ensureThinkingBlock` (~L1053, ONE `details.thinking`
+per message, idempotent; phase 109 D15 re-opens it on every later thinking frame),
+`closeThinkingBlock` (~L1075), `closeToolCalls` (~L1086), `appendToolLine`
+(~L1136, ONE `details.tool-calls-disclosure` per message — phase 117 D3
+open-live/fold-at-rest), `armToolLineClock` (~L1479, the phase-87 clock queries
+`.tool-calls .tool-call:last-child`), the turn handler in `runTurn`
+(thinking ~L3148 / tool ~L3193 / delta ~L3300 / done ~L3313 branches;
+`thinkingAcc` ~L3071, `toolAcc` ~L3080, `segRuns` — NEW — module scope beside
+them; the done save point ~L3355, the `tool_result` branch ~L3389, the
+stream-drop `finalizeFailedTurn` call ~L3417), `rememberBrainTurn` (L2589,
+`meta` spread — the pagehide partial save reuses it), `finalizeFailedTurn`
+(L2983); `renderStoredMessage` (~L2089: the `m.thinking` block + the `m.tools`
+loop, both rendered collapsed); `frontend/assets/shared.js` — `addThinkingBlock`
+(L126) + `addToolLines` (L175, the byte-parity copy, rendered closed);
+`app/schemas.py` — `ChatMessage` (L1103, `extra="forbid"`, phase-83 value caps,
+the wrap serializer that omits absent image keys), `ToolCall` (L1017),
+`HistoryTurn` (L58 — the history wire, UNCHANGED); `tests/e2e/mock_llm.py`
+(`_tool_flow` L1820, `_tool_call_stream` L3813, `_sse_stream` L3727,
+`compose_thinking` L3589, the trigger-dispatch order in `chat_completions`
+L3872 — the more-specific-phrase-wins convention); the E2E suites whose pins
+this phase updates (task 05): `test_turn_progress_loader.py` (the phase-109 D15
+re-open pin), plus the unit source pins in `test_frontend_feedback.py`,
+`test_frontend_turn_loader.py`, `test_frontend_tool_states.py`,
+`test_chat_persistence.py`, `test_shared_page.py`, `test_tool_call_compact.py`,
+`test_thinking_scroll.py`, `test_big_read_progress.py`, `test_read_range_tool_lines.py`,
+`test_read_truncation_frontend.py`, `test_search_tool_scope.py`,
+`test_frontend_failed_turn.py` (each pins `ensureThinkingBlock` / `appendToolLine`
+/ the clock in different depths — inspect each; ONLY the pins the redesign breaks
+change, the rest stay green untouched).
+
+## Bug basis (code-traced, 2026-10-04)
+The server streams the turn in true chronological order (`run_agent` yields per
+round: thinking → tool call → thinking → … → answer), but the client LUMPS:
+`app.js` funnels every thinking frame of the turn into ONE `details.thinking`
+block (`ensureThinkingBlock` is idempotent — the phase-109 D15 re-open re-opens
+that same block for each later agent round) and every tool frame into ONE
+`details.tool-calls-disclosure`. DOM order is therefore always
+`[ALL thinking] → [ALL tool calls] → [answer]` regardless of the actual order —
+the owner's "thought everything, then called all the tools, then answered"
+reading. The "thinking → answer → back to thinking" awkwardness is the D15
+re-open live: the model emits a short mid-round reply alongside a tool call
+(React style), the first `delta` closes the one thinking block and the answer
+starts, then the next round's thinking frame re-opens the SAME block above the
+tool lines — the answer begins, then thinking resumes on top of it. The persisted
+`bor.chat.v1` record only stores `thinking` (one concatenated string) + `tools`
+(one array) — the per-run order is never captured, so the shared page
+(`shared.js`) renders the same lumped layout, collapsed.
+
+## Objective
+Render each agent turn as a chronological timeline — each CONTIGUOUS run of
+thinking frames in its own `details.thinking` block, each CONTIGUOUS run of tool
+calls in its own `details.tool-calls-disclosure` (`Tool call(s) (N)` per run),
+segments in arrival order — live, on restore, and on the shared page; persist the
+run order in a new optional `segments` array on the brain record (additive;
+records without it — all pre-phase — restore byte-identically through the
+untouched legacy path).
+
+## Owner decisions (chat, 2026-10-04 — recorded per AGENTS.md rule 3)
+- **D1 — Per-run timeline.** Each contiguous thinking run = its own Thinking
+  block; each contiguous tool-call run = its own disclosure. Consecutive frames
+  of the same kind extend the current run; the first frame of a new kind closes
+  the previous run and opens the new one.
+- **D2 — Option B mid-round placement (owner-chosen, shown as a live DOM demo in
+  the owner's browser 2026-10-04).** ALL segments render ABOVE the answer
+  bubble, in arrival order — including runs that start AFTER the first `delta`
+  (the mid-round reply case). The bubble stays ONE element; its content
+  accumulates in arrival order (the mid-round text and the final answer are one
+  streamed text). Rejected: Option A (post-answer segments below the bubble —
+  the bubble grows above its own scratchpad).
+- **D3 — Plain `Thinking` label on every block (owner-chosen).** The phase-17
+  pinned summary literal stays byte-identical across runs (zero new literals;
+  position distinguishes the runs). The disclosure summary stays the phase-117
+  `Tool call(s) (N)` — now per run.
+- **D4 — Additive persistence.** The brain record gains an OPTIONAL `segments`
+  array; `thinking` (full concatenated text — feeds the history wire + the
+  per-turn log) and `tools` (all call records) are KEPT (old-client graceful
+  degradation; the phase-113 lesson applied up front). `segments` is omitted when
+  absent (the `undefined`-drops-the-key house pattern) — a no-thinking,
+  no-tools record stays byte-identical to pre-phase.
+- **D5 — Open live, fold at rest** (extends phase 117 D3 + the phase-17
+  open-while-thinking contract): the active run's block is OPEN while its frames
+  stream; a new run's first frame closes the previous run; the first `delta`,
+  `done`, and the stop/abort settle fold the open runs; the restore path and
+  the shared page render everything COLLAPSED.
+- **D6 — Server: a validated `segments` field on `ChatMessage`.**
+  `extra="forbid"` means the new key would 422 every saved-chat write without a
+  schema field (the phase-113 lesson: a missing key silently UNSAVED every
+  grounded brain record). The field is a discriminated union (`kind` =
+  `"thinking"` | `"tool"`) with phase-83-style value caps, omitted-when-`None`
+  in the serializer (the phase-50 round-trip contract). No migration (the record
+  is opaque JSONB), no SSE contract change, no history-wire change.
+
+## Design (shared by all tasks — the executor reads this, not the chat)
+
+### The `segments` entry shape (D4)
+```
+segments: [
+  { kind: "thinking", text: "<that run's full text>" },
+  { kind: "tool", name: "…", argument?: "…", offset?: int, limit?: int,
+    path?: "…", truncated?: true, chars_shown?: int, chars_total?: int },
+  …
+]
+```
+- One `thinking` entry per RUN (the run's accumulated text — the same text that
+  streams live into that run's block). One `tool` entry per TOOL CALL (the exact
+  `toolAcc` record shape — the phase-37 `{name, argument}` plus the phase-139
+  `offset/limit` and phase-146 `path` additive fields, and the phase-95
+  `truncated/chars_shown/chars_total` stamp when present).
+- Built at save time from the run tracker: an EMPTY thinking run stores NOTHING
+  (a zero-char run — e.g. a `BOR_STREAM_THINKING`-suppressed turn — is absent);
+  a turn with no thinking and no tools stores no `segments` key at all.
+- `thinking` (the full concatenation, for the history wire + the log) and `tools`
+  (every call record, for old clients) are UNCHANGED in the record.
+
+### `app/schemas.py` (task 01)
+- `ChatThinkingSegment`: `kind: Literal["thinking"]`, `text: str`
+  (`min_length=1`, `max_length=32_000` — `HistoryTurn`'s cap, phase 83).
+- `ChatToolSegment`: `kind: Literal["tool"]` + the EXACT `ToolCall` field set
+  (name/argument/offset/limit/path/truncated/chars_shown/chars_total with their
+  existing caps) — one model, no duplication of the field definitions where
+  practical (the docstring cross-references `ToolCall`).
+- `ChatSegment = Annotated[Union[ChatThinkingSegment, ChatToolSegment],
+  Field(discriminator="kind")]`.
+- `ChatMessage.segments: list[ChatSegment] | None = Field(default=None,
+  max_length=50)` (the phase-83 cap style — far past any realistic turn: the
+  round cap is 10 → ≤ 20 entries; 50 matches the `tools` cap).
+- The EXISTING wrap serializer (`_drop_image_when_absent`) gains the rule:
+  `segments is None → pop "segments"` (ABSENT, never `null` — the phase-50
+  contract; a record WITH segments keeps them). `HistoryTurn` and the
+  `history_to_messages` mapper are UNTOUCHED (segments never travel the wire —
+  the concatenated `thinking` travels exactly as today).
+
+### `frontend/assets/app.js` — the live turn (task 02)
+- Turn state: `segRuns = []` (module scope, reset in `runTurn` beside
+  `thinkingAcc`/`toolAcc` — an array of run objects
+  `{ kind, text, records }`), `currentRun = null` (turn-local).
+- **Insertion anchor (D2):** every run element is inserted `before`
+  `body.querySelector(".bubble")` (get-or-create the bubble first, as today).
+  There is no other anchor — segments ALWAYS sit above the bubble, in arrival
+  order. `ensureThinkingBlock`'s old `.tool-calls-disclosure ?? .tool-calls ??
+  .bubble` anchor is REPLACED by this.
+- **`thinking` frame (per frame):** `settleToolLine()` (unchanged);
+  `thinkingAcc += ev.text` + `sawThinking` + `clearTurnTimeout()` + `if (!wrap)
+  wrap = addMessage("brain","")` + `removeTyping()` (all unchanged). Then the
+  run logic: if `currentRun?.kind === "thinking"` → extend it (re-render
+  `renderMarkdown(run.text)` into THAT block's `.thinking-text` — the existing
+  pre-update pin-state / bottom-follow logic moves verbatim into this branch,
+  now per-block); else → close `currentRun` (if any, `details.open = false`),
+  create `details.thinking` (`open = true`, `<summary>Thinking</summary>` +
+  `.thinking-text`, inserted before the bubble), push `{kind:"thinking",text:"",
+  records:[]}` to `segRuns`, `currentRun` = it, extend.
+- **`tool` frame (per frame):** the existing guards stay byte-identical
+  (the phase-139 `frameOffset`/`frameLimit`, the phase-146 `framePath`
+  well-formedness; `toolAcc.push(toolRecord)`; `clearTurnTimeout()`; the
+  `toolStatus` label logic; the phase-70 legacy-name mapping). Then the run
+  logic: if `currentRun?.kind === "tool"` → extend that disclosure; else → close
+  `currentRun` (if any), create `details.tool-calls-disclosure` (`open = true`,
+  `summary.tool-calls-summary` + the `div.tool-calls` list `role=list`
+  `aria-label="Tool calls"`, inserted before the bubble), push
+  `{kind:"tool",text:"",records:[]}` to `segRuns`, `currentRun` = it; extend =
+  build the line EXACTLY as today (`appendToolLine` — now with the container
+  passed in: `appendToolLine(container, name, argument, offset, limit, scope)`,
+  the line bytes + the four pinned `line.textContent` label literals + the
+  phase-139 range suffix + the phase-146 scope span UNCHANGED, the summary
+  count updated per append — `Tool call(s) (N)` per run), then
+  `armToolLineClock(wrap, lineEl)` (the NEW signature — task 02's clock fix).
+- **`armToolLineClock(wrap, lineEl)` (the phase-87 multi-disclosure fix):**
+  store the `lineEl` reference (module scope, reset with the wrap); the interval
+  appends the `.tool-elapsed` suffix to `lineEl` instead of querying
+  `.tool-calls .tool-call:last-child` (that query breaks with multiple
+  disclosures — it would find the last line of the FIRST list). The visible
+  behavior is identical (the suffix on the newest line; `settleToolLine` still
+  removes every `.tool-elapsed` in the wrap + resets the reference).
+- **`delta` handler:** `settleToolLine()` + `acc += ev.text` + the
+  `thinking→streaming` transition UNCHANGED; replace
+  `closeThinkingBlock(wrap)` + `closeToolCalls(wrap)` with `closeCurrentRun()`
+  (folds `currentRun` if open; idempotent; no-op without a run).
+- **The other settle-pair sites — `finalizeFailedTurn`'s `if (wrap)` block
+  (L2990–L2991), the STOP path (L3477–L3478), and every remaining
+  `closeThinkingBlock(wrap); closeToolCalls(wrap);` pair (grep — the
+  redesign removes both functions):** `closeAllRuns(wrap)` (closes EVERY
+  open `details.thinking` + `details.tool-calls-disclosure` in the wrap —
+  defensive; by construction at most the last run is open, but a late
+  double-close must be a no-op). The rest of `done` is unchanged.
+- **Save payloads (the FIVE sites):** `buildSegments(segRuns)` (a helper —
+  maps runs: thinking run → `{kind:"thinking",text}` when non-empty; tool run
+  → one `{kind:"tool",…record}` per record, in order) — the `done` save point
+  (~L3355); the `finalizeFailedTurn` parameter + its `if (wrap)` saved record
+  (the two call sites — stream-drop ~L3431, network-error ~L3519 — pass
+  `buildSegments(segRuns)`); the STOP path's save meta (L3487–L3491,
+  `stopped: true`); the pagehide partial (L3642–L3650 — `segRuns` is module
+  scope, readable there). All include `segments` non-empty only. The
+  zero-frame fallback save needs nothing (zero frames → no runs → no key).
+  The `thinking`/`tools` keys are UNCHANGED at every site.
+- The UI state machine, `#send-status` copy, the 300 s pre-token guard, the
+  stream-drop guard, and the `thinking-without-answer` fallback are ALL
+  UNCHANGED (§7.4 never-stale intact). `BOR_STREAM_THINKING=0` needs no client
+  change (no thinking frames arrive → no thinking runs).
+
+### `frontend/assets/app.js` — the restore path (task 03)
+- `renderStoredMessage`: after the bubble exists, IF
+  `Array.isArray(m.segments) && m.segments.length` → `restoreTimeline(wrap,
+  m.segments)` and SKIP the legacy `m.thinking` block + the `m.tools` loop
+  (segments take precedence — they carry the same data in order); ELSE the
+  legacy path is BYTE-IDENTICAL (a pre-phase record — or a `BOR_STREAM_THINKING=0`
+  turn saved with the old client — restores exactly as today).
+- `restoreTimeline`: iterate `m.segments` in order; group CONSECUTIVE
+  `kind:"tool"` entries into ONE `details.tool-calls-disclosure` (created
+  CLOSED — D5; summary `Tool call(s) (N)`; each line through the SAME
+  `appendToolLine` container-signature path with the EXISTING tOffset/tLimit/tPath
+  guards + the existing `appendTruncatedNote` call for `t.truncated` records —
+  the current loop's guards move verbatim inside the grouping); a `kind:"thinking"`
+  entry → its OWN `details.thinking` (created CLOSED; `.thinking-text` =
+  `renderMarkdown(entry.text)` — the restore convention stays escape-first);
+  unknown `kind` values are SKIPPED (never render from storage — textContent
+  only, the house rule). All elements inserted before the bubble.
+
+### `frontend/assets/shared.js` — the shared page (task 03)
+- `addSegments(wrap, segments)` — the shared-page parity copy of
+  `restoreTimeline` (pure render, always COLLAPSED — D5): the same grouping,
+  the same line bytes (the four label literals + the phase-95 truncation note
+  + the phase-139/146 suffixes, already parity-pinned in `addToolLines`), the
+  same summary count; the `addThinkingBlock`/`addToolLines` legacy path is
+  BYTE-IDENTICAL when the record has no `segments`. The record-dispatch site
+  (~L456): `if (Array.isArray(m.segments) && m.segments.length)
+  addSegments(wrap, m.segments); else { the existing addThinkingBlock +
+  addToolLines }`.
+
+### `tests/e2e/mock_llm.py` (task 04)
+- `THINK_TOOLS_TRIGGER = "think out loud and use your tools"` — checked in the
+  streaming branch BEFORE the `_tool_flow` dispatch (the more-specific-phrase-wins
+  convention — the phrase contains both `think out loud` and `use your tools`,
+  so it must not fall through to the plain answer path; no other existing
+  trigger phrase is a substring of it, and no existing E2E question carries it —
+  verify both before wiring).
+- `_thinking_tools_flow(body)` — stateless, shaped like `_tool_flow` (gated on
+  the `tools` parameter + the `<tools>` section, like the other marker flows):
+  - request 1 (tools offered, no tool results yet): `thinking` =
+    `"Step 1: list the documents to find the reference server config."` →
+    `_tool_call_stream("ls", {}, "call_0", thinking=thinking)`;
+  - request 2 (a `tool`-role top-level source listing — the agent's `ls` tree
+    format, no file lines yet): `"Step 2: drill into the first source."` → the
+    `_drill_target` scoped `ls` (id `call_1`), with thinking;
+  - request 3 (a `tool`-role folder listing with file lines — parse the FIRST
+    file line's labeled `source:` / `path:` fields, the phase-63/70 format):
+    `"Step 3: read the file line's document."` → `read` on the JOINED
+    combined `source/path` (id `call_2`), with thinking;
+  - request 4 (a `tool`-role read result — content starting with the agent's
+    `"Document <source/path>:"` header): `"Step 4: compose the answer from the
+    read document."` → the phase-37 answer convention: `Read <source/path>.
+    <first 80 chars of the read document's content>` (content stream, with
+    thinking ahead of it).
+- `_tool_call_stream(name, arguments, call_id, thinking="")` — the optional
+  `thinking` param: when non-empty, yield `reasoning_content` chunks FIRST
+  (the 12-char split — the `_sse_stream` convention), then the existing
+  `tool_calls` frames + `finish_reason: "tool_calls"` (unchanged). Default
+  `""` → every pre-phase 3-arg caller streams BYTE-IDENTICAL.
+- Docstring: the new trigger entry (the phase-158 flow) — the mock stays
+  mock-only by design (`E2E_REAL_LLM` note unchanged).
+
+### `tests/e2e/test_thinking_timeline.py` (task 04 — dedicated suite, run in isolation)
+The conftest `app_server`/`page`/`seeded_kb` fixtures + the phase-37 admin
+login + the trigger question (the KB must be seeded so request 4's read result
+exists — mirror `test_agent_document_tools.py`). Six tests:
+1. **`test_timeline_order_after_completed_turn`** — after `done`: the brain
+   wrap's `.msg-body` children before the bubble are EXACTLY
+   `[details.thinking, details.tool-calls-disclosure, details.thinking,
+   details.tool-calls-disclosure, details.thinking, details.tool-calls-disclosure,
+   details.thinking]` (7 elements); the four `.thinking-text`s carry DISTINCT
+   `Step 1`…`Step 4` markers (distinctness = the runs are separate blocks, not
+   one lump); each disclosure summary is `Tool call (1)`; the answer bubble
+   carries the `Read <path>` echo.
+2. **`test_runs_fold_at_rest`** — after `done`: NO `.thinking` /
+   `.tool-calls-disclosure` has the `open` attribute; the summaries are
+   visible (D5).
+3. **`test_live_runs_open_while_streaming`** — during the turn (an
+   `expect.poll` predicate over the mock's 0.1 s pacing window): at least one
+   `.thinking` or `.tool-calls-disclosure` is `open` while the answer bubble is
+   still empty (the D5 live-open contract — the live feedback the owner keeps).
+4. **`test_restored_timeline_and_record`** — RELOAD (same context): the
+   restored message renders the same 7-element timeline, all closed; the
+   localStorage `bor.chat.v1` record for that brain turn carries a `segments`
+   array of EXACTLY 7 entries in the pattern
+   `thinking, tool, thinking, tool, thinking, tool, thinking` (4 thinking runs
+   + 3 tool entries).
+5. **`test_shared_page_timeline`** — the phase-51 save + share flow, a FRESH
+   context on `/shared/<token>`: the same 7-element timeline renders, all
+   collapsed (the `shared.js` parity — `addSegments`).
+6. **`test_no_thinking_turn_single_disclosure`** — a plain `use your tools`
+   question (NO thinking trigger): the turn renders EXACTLY ONE
+   `.tool-calls-disclosure` (3 lines, `Tool calls (3)`) and ZERO `.thinking`
+   (the run-grouping contract: no thinking frames → one tool run — the
+   phase-117 behavior for no-thinking turns is preserved).
+
+## Tasks
+1. `01_schema_segments.md` — the discriminated `ChatSegment` models + the
+   `ChatMessage.segments` field + the serializer omission + the integration
+   contract (accept / caps / byte-identical round-trip / shared read).
+2. `02_live_timeline.md` — the per-run live rendering (run tracker, D2 anchor,
+   the clock re-target, the settle sites, the save payloads) + the JS source
+   unit pins.
+3. `03_restore_and_shared.md` — the `restoreTimeline` dispatch in
+   `renderStoredMessage` + the `shared.js` `addSegments` parity + the unit pins.
+4. `04_mock_and_e2e.md` — the mock `THINK_TOOLS_TRIGGER` flow + the dedicated
+   `test_thinking_timeline.py` story suite, run in isolation.
+5. `05_regression_update_and_commit.md` — the phase-109 suite pin update + the
+   remaining unit-pin updates, the full gate, the documentation pass, the
+   atomic commit, the phase move.
+
+## Testing & Quality
+- Unit (new): `tests/unit/test_thinking_timeline.py` — the source-level pins:
+  the per-run creation (a NEW `details.thinking` when the run kind changes,
+  insert-before-bubble anchor — D2), the plain `Thinking` literal (D3), the
+  per-run disclosure + the `Tool call(s) (N)` per-run count, the
+  `armToolLineClock` reference (the `:last-child` query is GONE), the
+  `segRuns` → `buildSegments` mapping (empty-run skip, the tool-record shape),
+  the `delta` `closeCurrentRun` + the settle-pair sites → `closeAllRuns`, the
+  FIVE save-payload sites (done / finalizeFailedTurn + its 2 call sites /
+  stop path / pagehide), the restore dispatch (segments vs legacy — the
+  legacy path byte-identical), the `shared.js` `addSegments` parity, and
+  `innerHTML` ABSENT from the restore/shared builders (the house rule).
+- Integration: `tests/integration/test_chats_api.py` (extended) — a record WITH
+  segments (both kinds, every additive tool field) is accepted and round-trips
+  through create/get; `segments` > 50 → 422; a thinking-segment text > 32 000 →
+  422; an unknown segment `kind` → 422 (`extra="forbid"` intact — a stray
+  `<b>`-ish key still 422s); a record WITHOUT `segments` round-trips with the
+  key ABSENT (never `null` — the phase-50 byte-identical contract, pinned);
+  the shared read (`/api/chats/<id>/shared` or the public read path) carries
+  segments (the public shape).
+- Existing unit suites MUST stay green: every pin NOT broken by the redesign
+  (the tool-line label literals, the phase-117 deboxed CSS, the phase-87
+  `.tool-elapsed` behavior, the phase-139/146 suffix pins, the emoji guard,
+  the `test_tool_call_compact.py` pins — a no-thinking turn is one run, so the
+  phase-117 E2E contract is UNCHANGED).
+- E2E: `tests/e2e/test_thinking_timeline.py` (new — the six tests above), green
+  **in isolation** (`uv run pytest tests/e2e/test_thinking_timeline.py -v
+  --no-cov`), mock-only.
+- Regression E2E (task 05, in isolation): `test_thinking_display.py` (a
+  no-tools thinking turn is ONE run — the suite's contract is unchanged),
+  `test_tool_call_compact.py` (unchanged — no-thinking single-run),
+  `test_turn_progress_loader.py` (UPDATED in task 05 — the D15 pin → the
+  per-run contract), `test_big_read_progress.py` (the clock's visible behavior
+  is identical — must stay green UNCHANGED), `test_agent_document_tools.py`,
+  `test_share_chat.py`, `test_chat_persistence.py`, `test_smoke.py`.
+- Coverage: `uv run pytest --cov=app --cov-report=term-missing` **>90%** on
+  `app/` (task 01's schema code is unit/integration-covered; the rest is held
+  by the suite).
+- Lint/types: `uv run ruff check . && uv run pyright` clean.
+- The phase is "Complete" only when the **entire** project test suite passes
+  100% (every test in the project, not just this phase's).
+
+## Documentation & Consistency
+- The final pass reviews `README.md` and `AGENTS.md` in full against the
+  project as it stands after this phase — fixing every inconsistency found,
+  **including pre-existing ones not caused by the phase**.
+- Tasks update `README.md`/`AGENTS.md` immediately when their own changes are
+  user-visible (the timeline is a visible UI change — name it where the chat
+  thinking/tool-call display is described, if anywhere).
+
+## Completion Criteria
+- [ ] A completed tool+thinking turn renders `Thinking → Tool call (1) →
+      Thinking → Tool call (1) → … → answer` — the E2E's 7-element order pin
+      (task 04 test 1); the runs fold at rest (test 2) and stay open while
+      streaming (test 3).
+- [ ] A reload restores the same timeline + the record's `segments` array
+      (test 4); a fresh context on `/shared/<token>` renders the same timeline
+      (test 5).
+- [ ] A no-thinking tool turn is ONE disclosure, 3 lines (test 6) — the
+      phase-117 contract is preserved; `test_tool_call_compact.py` +
+      `test_thinking_display.py` + `test_big_read_progress.py` green in
+      isolation UNCHANGED.
+- [ ] A pre-phase saved record (no `segments`) restores byte-identically
+      (the integration pin + the E2E regression suites).
+- [ ] `uv run pytest` green (100% of the project suite);
+      `uv run pytest --cov=app --cov-report=term-missing` > 90%;
+      `tests/e2e/test_thinking_timeline.py` green in isolation;
+      `uv run ruff check . && uv run pyright` clean.
+- [ ] `git diff --stat` limited to `app/schemas.py`, `frontend/assets/app.js`,
+      `frontend/assets/shared.js`, `tests/`, and the phase files.
+- [ ] README.md and AGENTS.md are accurate and consistent with the whole
+      project (verified in the final pass).
+- [ ] ONE owner-directed exception to "no behavior change in completed phases":
+      the phase-109 D15 re-open contract is REPLACED by the per-run blocks
+      (owner direction 2026-10-04 — recorded above); `test_turn_progress_loader.py`'
+      pin is updated in task 05 to the per-run contract (two thinking blocks,
+      each carrying its own round, open in its live window, folded at rest).
+- [ ] One atomic `--no-gpg-sign` commit (below); the phase dir moved to
+      `.agents/phases/complete/`.
+
+## Commit
+```bash
+git add -A .agents/ app/schemas.py frontend/ tests/ README.md && git commit --no-gpg-sign -m "feat(ui): render thinking and tool runs as a chronological timeline (per-run blocks, segments persistence)"
+```
+
+## Locked decisions
+- **The SSE contract is UNCHANGED (A15 intact).** The frames already arrive in
+  true chronological order (`run_agent`'s yield order — verified in code); this
+  phase is client-grouping + record persistence only. `app/rag/` is untouched.
+- **D1–D6 (owner, 2026-10-04)** — the per-run timeline, Option B placement,
+  the plain `Thinking` label, the additive `segments` record, open-live/
+  fold-at-rest, and the validated `ChatMessage.segments` field (the
+  `extra="forbid"` boundary preserved with phase-83-style caps).
+- **A10 history wire UNCHANGED** — segments never travel to the LLM (the
+  concatenated `thinking` travels as `reasoning_content` exactly as today;
+  `HistoryTurn` + the mapper are untouched).
+- **A13 UNCHANGED** — no migration (the record is opaque JSONB; the schema
+  field is validation at the boundary only).
+- **A16 honoured** — one new story E2E suite + the task-05 regression updates;
+  mock-only by design. **A17 honoured** — one atomic `--no-gpg-sign` commit.
+- **The phase-87 clock re-target** (the `:last-child` query → the tracked
+  reference) is a bug fix in service of D1; its visible behavior (the suffix on
+  the newest line) is byte-identical — `test_big_read_progress.py` stays green
+  unchanged. No other anchor changed.