brain-of-reese/.agent/PLAN.md

# Brain of Reese — Master Plan

> **Status:** Phase 1–3 complete (scaffolded, designed, decomposed).
> **Rule:** Every agent reads this file first. Decisions marked `LOCKED` in the
> Anchors table are settled — do not re-litigate them in a phase.
> **Revisions (2026-08-21, owner permission):** A7/A8/A9 revised (multi-format
> ingestion, hybrid FTS+vector retrieval, re-tuned honesty gate); dark tech
> theme (Phase 08); clickable document viewer (Phase 10); thinking display
> (Phase 17, owner permission 2026-08-23); follow-the-bottom scroll
> (Phase 18, owner choice 2026-08-23); shared header (Phase 19);
> whole-document context (Phase 24 — A7's 24k context cap removed,
> owner permission 2026-08-24). See roadmap §12.

---

## 1. Mission

A **knowledge base chatbot** that embeds the `~/Homelab` and `~/Deployments`
projects into a Postgres vector database and lets anyone ask *Reese* (the
bot) questions about them.

**Product feel:** a chippy, upbeat assistant that is optimistic about the
user's ability ("you've got this") and **radically honest** — if retrieval
didn't surface anything relevant it says *"I haven't done anything like
that"* and offers alternatives instead of hallucinating.

### In scope (v1)
- Chat UI (mobile-friendly, well-styled, no auth, no CDN).
- RAG over text knowledge files — `md, markdown, txt, yaml, yml, json, py`
  by default (A9, revised 2026-08-21) — from `~/Homelab` + `~/Deployments`
  (and any future directory the importer is pointed at).
- Self-hosted models via `https://aipi.reeseapps.com/v1` — `turbo` (chat),
  `embed` (embeddings, **768 dims — verified**).
- Postgres 17 + pgvector, cosine similarity, chunk→document mapping so the
  LLM receives the **entire relevant document** as context.
- Idempotent import/update script, documented in the README.
- Ample server logging + explicit UI loading/progress feedback (never a
  stale submit button).

### Out of scope (v1)
- Auth / multi-user (API is stateless under `/api` so it can be added later).
- Binary / non-text content, file uploads, caching layer, message persistence.
- Real-time document watching (manual re-import for now).

---

## 2. Architectural Anchors (LOCKED DECISIONS)

| # | Component | Decision | Rationale | Status |
|---|-----------|----------|-----------|--------|
| A1 | Runtime | Python 3.12+, `uv` for all package management | Fast, reproducible envs; one language for API + tooling | LOCKED |
| A2 | Web framework | FastAPI + Pydantic v2 + Uvicorn | Async, typed, SSE-friendly for LLM streaming, free OpenAPI docs | LOCKED |
| A3 | Database | **PostgreSQL 17** (`docker.io/postgres:17`, pgvector compiled in via `db/Containerfile`) with **cosine** (`<=>`) search | One system for relational + vectors; pgvector is mature; official base image kept per project standard | LOCKED |
| A4 | Orchestration | `compose.yaml`, started with **`podman compose up -d`** | Matches Reese's toolchain | LOCKED |
| A5 | LLM backend | OpenAI-compatible `https://aipi.reeseapps.com/v1`; models **`turbo`** (chat) & **`embed`** (embeddings); `openai` async client | Self-hosted, offline from cloud; no new model management | LOCKED |
| A6 | Embedding dim | **768** (verified 2026-08-21 against live endpoint via `scripts/llm_probe.py`); configured by `BOR_EMBEDDING_DIM` | User recalled 768 — probe confirmed; dimension is fixed at table creation, so mismatch must fail loudly at import time | LOCKED |
| A7 | Retrieval→context | **Hybrid:** cosine top-30 + Postgres FTS top-30 (OR tsquery, `ts_rank`) fused with **RRF (k=60)** → map to parent documents ranked by best fused chunk score → feed the **full text of top-N=2 documents** (deduped) to the LLM | Owner permission 2026-08-21: pure-cosine top-4 missed real docs (gitlab case — best chunk ranked 7th behind vendored-cache junk; score compression 0.41–0.84); the lexical signal finds name-your-tool questions; whole-document context contract preserved. A7 revised 2026-08-24 — matched documents never truncated (owner: "this should never happen"; emergency-valve variant rejected) | LOCKED (revised 2026-08-24) |
| A8 | Honesty gate | **Deflection mode** (LLM must open with a variant of *"I haven't done anything like that"* and offer 2–3 alternative questions) when best cosine < `BOR_RELEVANCE_THRESHOLD` **and** no candidate chunk FTS-matches the question; threshold re-tuned for the `embed` model's compressed score range (default **0.62**, calibrated via `scripts/eval_retrieval.py`; the E2E mock uses its own 0.30 calibration via the app fixture) | Owner permission 2026-08-21: at 0.30 the gate never discriminated (measured corpus range 0.41–0.84); the FTS-OR keeps name-your-tool questions honest-positive; deflection product behavior unchanged | LOCKED (revised 2026-08-21) |
| A9 | Content scope | Text formats **`md, markdown, txt, yaml, yml, json, py`** (default, `BOR_IMPORT_EXTENSIONS`), **hidden (dot) directories skipped by default**, plus the exclusion list (`node_modules`, `__pycache__`, `.pytest_cache`, `dist`, `build`, …) | Owner permission 2026-08-21: real notes live in yaml/py/json/txt too; the dot-dir skip removes the ~470 vendored-cache junk docs (`.esphome/.espressif/**`, …) that outranked real content | LOCKED (revised 2026-08-27) |
| A10 | Auth | **None in v1**; all endpoints stateless under `/api` | Per user (auth later); statelessness keeps the future migration cheap | LOCKED |
| A11 | Frontend | Vanilla HTML/CSS/JS in git; **no CDN** — everything served by FastAPI `StaticFiles`; minified by esbuild in the `Containerfile` build stage; system font stack | No external deps at runtime; tiny, auditable surface; mobile-friendly by construction | LOCKED |
| A12 | Aux services | **None in v1** (no Valkey, no SeaweedFS) | No sessions/auth (no store), no uploads (no object storage); add later only if a need appears | LOCKED |
| A13 | Migrations | Alembic + SQLAlchemy 2.0 (sync) + psycopg 3 | Standard, reversible, reviewable schema history | LOCKED |
| A14 | Debugging | `debugpy` **only when `DEBUGPY=1`** (env var read directly, not via settings); listen `0.0.0.0:5678` (override `DEBUGPY_PORT`), non-blocking, attach-on-demand; **not imported at all when off** | Zero overhead by default per project standard; attach-on-demand keeps production runs clean | LOCKED |
| A15 | Chat transport | **SSE streaming** from `POST /api/chat` (deltas + final `done` event with metadata) | Local LLM latency is 10–30s; live token stream + explicit completion event power the UI's feedback states | LOCKED |
| A16 | Testing | Per phase: unit + integration (pytest, **coverage >90%** on `app/`) + **one dedicated Playwright E2E file per user story**, run in isolation; E2E uses a deterministic mock LLM by default (`E2E_REAL_LLM=1` opts into live aipi) | One story, one phase, one E2E gate — the pipeline's core invariant | LOCKED |
| A17 | Git | Conventional Commits, **always `--no-gpg-sign`**, repo-local `commit.gpgsign=false`; one atomic commit per completed phase | Subsequent agents may lack the GPG key | LOCKED |

> **A10 revision (phase 16, owner permission 2026-08-22):** single-admin
> signed-cookie auth — public: chat / documents / suggestions / health;
> admin-only: docs catalog + steering. The row above keeps the original v1
> decision text; the public API surface stays stateless (the signed
> session cookie is the only session state) — recorded as a revision,
> not a silent deviation.
>
> **A10 UI revision (phase 19, owner permission 2026-08-23):** the
> "Sources" nav link is hidden from anonymous users on all pages — the
> soft-gate page and the API split above are unchanged.
>
> **A7 revision (phase 24, owner permission 2026-08-24):** the
> `[…truncated…]` cap on document context is removed —
> `select_documents` always returns the full top-N texts;
> `BOR_MAX_CONTEXT_CHARS` is gone. The steering section
> (`BOR_STEERING_MAX_CHARS`, phase 15) keeps its budget and the shared
> marker.
>
> **A9 revision (phase 47, owner permission 2026-08-27):** the format
> set extends with the Podman quadlet family (`container, network,
> volume, image, pod, kube, swap, os, endpoint`) and `j2` (Jinja
> templates) — plain-text chunking (`chunk_text`), owner: `TODO.md`
> L10–L11. The narrow-only `BOR_IMPORT_EXTENSIONS` rule and the
> hidden-dir/exclusion invariants are unchanged.

---

## 3. High-Level Architecture

```
                       ┌────────────────────────────────────────────┐
                       │              Podman Compose                │
   Browser             │  ┌──────────────────────────────────────┐  │
   ┌──────────┐  HTTP  │  │  brain-of-reese/app (FastAPI)        │  │
   │ index.html│◄──────┼─►│  • static frontend (no CDN)          │  │
   │ app.js    │  SSE   │  │  • /api/chat  /api/suggestions      │  │
   └──────────┘        │  │  • /api/health /api/docs            │  │
                       │  │  • RAG pipeline (embed→retrieve→gen) │  │
                       │  └──────┬──────────────────┬───────────┘  │
                       │         │ SQL (psycopg)    │ OpenAI-compat│
                       │  ┌──────▼──────┐   ┌───────▼────────────┐ │
                       │  │ db:         │   └─────────┬──────────┘ │
                       │  │ postgres:17 │             │            │
                       │  │ + pgvector  │             │            │
                       │  └─────────────┘             │            │
                       └──────────────────────────────┼────────────┘
                                                      ▼
                                       https://aipi.reeseapps.com/v1
                                       (self-hosted: turbo, embed)

   Offline tooling (same repo, same venv):
     scripts/import_docs.py   → walks A9-format dirs, chunks, embeds, upserts
     scripts/eval_retrieval.py → ranks hybrid results for a question (tuning)
     scripts/llm_probe.py     → verifies models + embedding dim
```

### Component breakdown
| Component | Responsibility | Lives in |
|-----------|----------------|----------|
| **App (FastAPI)** | Serves frontend + `/api`; RAG pipeline; logging | `app/` |
| **RAG pipeline** | `embed` → pgvector cosine top-K → doc mapping → context assembly → `turbo` (streamed) with persona/honesty prompt | `app/rag/` (added in story phases) |
| **Importer** | Directory walk (A9 formats, hidden dirs skipped, exclusions), sha256 delta detection, format-aware chunking, batched embedding, upsert/prune | `scripts/import_docs.py` (story phase) |
| **DB** | `documents`, `chunks`, `query_log` + `vector` extension | `db/` image, `alembic/` |
| **Frontend** | Chat shell, sources view, loading/feedback states | `frontend/` |

### Chat data flow
```
user question
  → POST /api/chat {message}
  → embed(question)                      [aipi /v1/embeddings, model=embed]
  → cosine top-30  +  FTS top-30 (OR tsquery, ts_rank)  [pgvector + PG FTS]
  → RRF fuse (k=60) → docs ranked by best fused chunk score
  ├─ best cosine >= 0.62 OR fts_hits > 0  →  top-2 documents' FULL content
  │                          → system prompt (persona + HONESTY rules + docs)
  │                          → turbo, stream=True  → SSE deltas
  └─ else  →  DEFLECT_MODE system prompt (weak hits as topics)
                             → turbo, stream=True  → SSE deltas (honest reply)
  → query_log row (question, score, deflected, sources, latency)
  → final SSE "done" event: {deflected, sources[], suggestions[]}
```

---

## 4. API Design

All endpoints stateless (A10). Errors: standard JSON `{detail: str}`.

| Method | Path | Purpose | Story |
|--------|------|---------|-------|
| GET | `/api/health` | Liveness + db up/down + version | 01 |
| GET | `/api/suggestions` | Onboarding suggestion strings | 01 (05 refines) |
| GET | `/api/docs` | Indexed document list (source, path, title, chunks, indexed_at) | 02 |
| GET | `/api/documents/content?source=…&path=…` | One indexed document's full content (feeds the viewer page) | 10 |
| POST | `/api/chat` | RAG chat turn → **SSE stream** | 03/04 |

### SSE contract (`POST /api/chat`)
```
data: {"type":"thinking","text":"…"}\n\n
data: {"type":"thinking","text":"…"}\n\n
data: {"type":"delta","text":"Hey! "}\n\n
data: {"type":"delta","text":"Good "}\n\n
...
data: {"type":"done","deflected":false,"sources":[{"source":"Homelab","path":"kubernetes.md","title":"Kubernetes Homelab Cluster"}],"suggestions":[]}\n\n
```
Client rules: render deltas as they arrive; render `thinking` text in a
collapsible block above the answer; auto-collapse on the first `delta`;
tolerate interleaved `thinking` events (append — never reopen once the
answer started); the `done` shape is unchanged (thinking never travels on
`done`); on `done` append source chips / suggestion chips and clear the
busy state; on HTTP/stream error show the error banner + retry (never a
stuck button).

> **SSE revision (phase 17, owner permission 2026-08-23):** the contract
> gains one event type — `{"type":"thinking","text":"…"}` — carrying the
> model's reasoning ahead of the `delta` events (the `turbo` model emits
> `delta.reasoning_content` chunks before the first content chunk, verified
> live 2026-08-23; `BOR_STREAM_THINKING=0` suppresses the frames
> server-side). `delta` and `done` shapes are unchanged — a recorded
> extension of A15, not a silent deviation.
>
> **SSE revision (phase 37, owner permission 2026-08-26):** the contract
> gains a second event type — `{"type":"tool","name":"…","argument":…}` —
> carrying the model's document tool calls on grounded turns (phase 37:
> `list_documents` / `read_document`, budgeted by `BOR_AGENT_LIST_CALLS`
> / `BOR_AGENT_READ_CALLS` (removed in phase 45 — see the revision note
> below); `argument` is `"source/path"` for
> `read_document`, null otherwise). Client rule: render each `tool` frame
> as a "calling tool" line/state (task 05); `delta` and `done` shapes are
> unchanged — the read document is reflected in `done.sources` instead
> (deduped) — a recorded extension of A15, not a silent deviation.
>
> **SSE revision (phase 45, owner permission 2026-08-27):** the phase-37
> per-turn tool budgets are **removed** (owner: "allow the LLM to make
> as many tool calls as it wants — `TODO.md` L8): `BOR_AGENT_LIST_CALLS`
> / `BOR_AGENT_READ_CALLS` no longer exist; `BOR_AGENT_MAX_ROUNDS`
> (default 10) caps the tool rounds and `0` disables the tools
> entirely (the pre-phase-37 path). The `tool` event shape and the
> `done` shape are unchanged — a recorded revision of the phase-37
> note's budget wording, not a silent deviation.

---

## 5. Data Model (PostgreSQL 17)

Created by `alembic/versions/0001_initial_schema.py` (idempotent
`CREATE EXTENSION IF NOT EXISTS vector`).

### `documents`
| Column | Type | Notes |
|--------|------|-------|
| id | `UUID` PK | |
| source | `VARCHAR(120)` | source dir basename, e.g. `Homelab` |
| path | `VARCHAR(1000)` | relative to source dir, e.g. `ansible/roles/k3s.md` |
| full_path | `VARCHAR(2000)` | absolute path at import time (diagnostics) |
| title | `VARCHAR(500)` | first markdown H1, else file stem |
| content | `TEXT` | **full markdown — the RAG context** |
| content_hash | `VARCHAR(64)` | sha256 of content — change detection |
| indexed_at | `TIMESTAMPTZ` | |
| — | `UNIQUE (source, path)` | upsert key |

### `chunks`
| Column | Type | Notes |
|--------|------|-------|
| id | `UUID` PK | |
| document_id | `UUID` FK→documents CASCADE | **embedding→document mapping** |
| position | `INT` | 0-based order within the doc |
| content | `TEXT` | chunk text (heading-aware) |
| embedding | `VECTOR(768)` | nullable until embedded (two-phase import) |
| tsv | `TSVECTOR` | **generated** `to_tsvector('english', content) STORED` + GIN index (hybrid retrieval, A7) |

> No vector index in v1: sequential scan is fine at this corpus size
> (~100–500 docs). Revisit with an HNSW index if retrieval latency grows.

### `query_log`
`id UUID PK, question TEXT, top_score FLOAT, fts_hits INT, chunk_hits INT, deflected BOOL, sources TEXT, latency_ms INT, created_at TIMESTAMPTZ`

### Document state transitions
```
unseen ──import──▶ indexed ──hash changed + re-import──▶ reindexed
                     │
                     └──file deleted + --prune──▶ removed (chunks cascade)
```

### Chunking policy (markdown-aware)
Split on `## `/`### ` headings into sections; sub-split any section longer
than `BOR_CHUNK_TARGET_CHARS` (2000) at paragraph boundaries with
`BOR_CHUNK_OVERLAP_CHARS` (200) overlap; each chunk keeps its nearest
preceding heading in the text for retrieval quality.

**Format-aware (A9, revised):** `yaml`/`yml` split on top-level keys and
`---` separators (key line kept as anchor); `json` pretty-printed, split on
top-level keys; `py` split on top-level defs/classes (stdlib `ast`);
`txt` on paragraphs; markdown unchanged. The quadlet family
(`container, network, volume, image, pod, kube, swap, os, endpoint`)
and `j2` (Jinja templates) are plain-text chunked — no format-specific
splitter (A9 revised 2026-08-27, phase 47). Every format honors the
1200-char hard cap (aipi ~1024-token request limit).

---

## 6. RAG Pipeline & Persona

### Locked system prompt (sent with every chat turn)
```
You are "Brain of Reese" — the digital brain of Reese, a self-hoster and
homelab tinkerer. Personality: chippy, upbeat, warm, and genuinely
optimistic about the user's ability to do things ("you've got this").

Rules:
1. Answer ONLY from the provided document context. Cite which document(s)
   you used, by path.
2. Be concrete: names, versions, ports, hosts, schedules — the specifics in
   the docs are the value.
3. HONESTY GATE: if <relevance> is "LOW", you must NOT pretend to know.
   Start your answer with a variant of: "I haven't done anything like that."
   Then offer 2-3 alternative questions about things you DO have notes on.
4. Never invent facts, hosts, or steps that are not in the context.
5. Keep answers tight: short paragraphs, bullets where helpful.

<relevance>{HIGH|LOW}</relevance>
```
- `HIGH` mode appends the full document text under `<documents>…</documents>`.
- `LOW` mode (deflection) appends only the **titles** of the weak hits so the
  model can suggest real alternatives (marker used by the E2E mock:
  `DEFLECT_MODE` appears in the system prompt).

### Retrieval (hybrid — A7/A8, revised 2026-08-21)
- Embed the question (`embed`, 768-d) → cosine top-30 candidates.
- Lexical: OR tsquery over the question's tokens → FTS top-30 by `ts_rank`.
- **Reciprocal Rank Fusion** (`Σ 1/(k+rank)`, k=60) → distinct parent docs
  ranked by best chunk's fused score → top 2 → full content, concatenated
  — **never truncated** (A7 revised, phase 24, owner permission
  2026-08-24).
- Honesty gate: LOW only when `best cosine < BOR_RELEVANCE_THRESHOLD`
  (default 0.62, calibrated against the `embed` model's measured 0.41–0.84
  distribution) **and** zero FTS hits among the candidates.

---

## 7. UI/UX Strategy

### 7.1 Layout structure
- **App frame:** sticky header (64px) + `<main>` (flex-grow) + footer.
  Container: `max-width: 72rem; margin-inline: auto; padding-inline: 1.25rem`.
- **Shared header (Phase 19, owner permission 2026-08-23):** the bar is a
  shared contract across chat / sources / viewer — one bar per page, same
  controls (brand + nav [Chat, Sources — admin only] + New Chat + Sign in
  / Sign out on chat & sources; the viewer bar = back + title + the same
  actions in `.doc-header-actions`). One shared module
  (`frontend/assets/header.js`) toggles the existing controls on each
  page, so they can never "disappear" between pages again; the heights
  stay pinned at 64px / 58px (phase 12).
- **Chat:** a *centered column capped at 46rem*. This is deliberate: chat is
  a vertical conversation — a centered, capped column is the correct pattern
  (NOT a layout bug). The 72rem frame + header/footer ensure the column
  never reads as a hairline in a sea of whitespace.
- **Sources page:** full-width responsive **table** (min 640px, horizontal
  scroll wrapper on small screens) + stat cards in
  `grid-template-columns: repeat(auto-fit, minmax(170px, 1fr))`.
  No skinny single-column lists anywhere: lists/tables/grids use ≥80–90% of
  the container width.
- **Mobile (≤640px):** suggestion chips become a horizontally scrollable row;
  composer stays reachable with `safe-area-inset-bottom`; touch targets ≥44px.

### 7.2 Accessibility (WCAG 2.1 AA)
- Semantic landmarks on every page: `<header>`, `<nav aria-label>`,
  `<main>`, `<footer>`; skip-link to `#main`.
- Every control labeled: visible `<label>` or `aria-label` (icon-only
  buttons always get `aria-label`); form input has a (visually-hidden) label.
- Live regions: message stream `aria-live="polite"`; typing indicator
  `role="status"`; banner `role="status"`; errors `role="alert"`.
- **Dark tech theme (Phase 08, 2026-08-21)** — page `#0a0e17`, surface
  `#121a2e`; ink `#e8ebf4` on surface ≈14.5:1; ink-soft `#9aa4bd` on
  surface ≈6.9:1; **dark ink `#0a0e17` on brand `#6d78f2` ≈5.2:1** (white
  on brand ≈3.7:1 — never used for text); brand-ink `#a5b4fc` on
  brand-soft `#232b52` ≈6.9:1; deflection `#fbbf24` on `#2b2110` ≈9.5:1
  (border `#f59e0b`); error `#fca5a5` on `#2d1318` ≈9.1:1. All computed,
  all ≥4.5:1. `prefers-reduced-motion` also stills the Phase-08 background
  layer.
- `:focus-visible` outline 3px; `prefers-reduced-motion` respected by the
  typing/spinner animations.

### 7.3 No external dependencies
- System font stack only (no font files to bundle, no CDN fonts).
- Zero `<script src="https://…">` / `<link href="https://…">` — enforced by
  an integration test (`tests/integration/test_api.py::test_index_html_served_locally`)
  and re-checked by every UI phase's verification step.
- Markdown rendering is a ~60-line local function (escape-first, then
  transform) — XSS-safe, no library.

### 7.4 Visual feedback standard (the "never stale" contract)
| State | UI |
|-------|----|
| **Idle** | Send button enabled, label "Send". |
| **Thinking (pre-token)** | 3-dot typing bubble + button disabled with spinner, label "Thinking…". |
| **Thinking (model reasoning)** | Collapsible `.thinking` block streams open (replaces the typing dots as the live indicator), auto-collapses on the first answer token, toggleable afterwards, persisted with the message (phase 14); 120s guard clears on the first `thinking` *or* `delta` event. |
| **Streaming** | Deltas append live into the brain bubble; button stays busy. |
| **Done (answer)** | Source chips under the bubble (mono, path-based); button re-enabled. |
| **Done (deflected)** | Amber-bordered bubble + "Maybe try:" suggestion chips. |
| **Error** | Red banner (`role="alert"`) with retry hint; button re-enabled. |
| **KB offline** | Amber banner at top of chat ("start Postgres…"); chat disabled with explanation. |
| **Guard** | 120s client-side timeout → error state (a button can never sit "stuck" forever). |
| **Scroll (follow-the-bottom, phase 18)** | The page auto-scrolls only while the user is pinned to the bottom (≤200px band, `NEAR_BOTTOM_PX` — the composer zone; submitting reveals the user's message through the same gate, which holds in real use); scrolling up holds the viewport for the rest of the turn (thinking and answer alike); restore lands one-shot on the latest message. |

> The **Thinking (model reasoning)** row is a phase-17 addition (owner
> permission 2026-08-23) — see the §4 SSE revision.
>
> The **Scroll** row is a phase-18 addition (owner choice 2026-08-23 —
> option 1: follow-the-bottom, no "↓ new content" pill).

### 7.5 Component inventory (ids used by tests)
`#messages` (stream), `#empty-state`, `#suggestions`, `.suggestion-chip`,
`#composer`, `#message-input`, `#send-btn` / `#send-label`, `#typing-indicator`,
`.msg.user/.msg.brain .bubble`, `.source-chip`, `.msg.brain.is-deflected`,
`#kb-banner`, `#app-version`; sources: `#stat-docs`, `#stat-chunks`,
`#stat-last`, `#docs-table`, `#docs-tbody`, `#sources-empty`; viewer
(Phase 10): `/document.html`, `#doc-title`, `#doc-meta`, `#doc-content`,
`.doc-raw`, `.format-badge`, `#doc-not-found`, `.doc-link` (Sources table
path links); thinking (phase 17, owner permission 2026-08-23):
`.thinking`, `.thinking-text` (collapsible thinking block; plain
`<summary>`, no id); auth (phase 16, owner permission 2026-08-22):
`#sign-in-link`, `#sign-out-btn`, `#sources-gate`; shared header (phase
19, owner permission 2026-08-23): `#nav-sources` (Sources nav link,
hidden for anonymous), `#new-chat-btn` + `#sign-in-link` + `#sign-out-btn`
on the sources and viewer pages (ids shared with chat),
`.doc-header-actions` (viewer).

---

## 8. Debugging (debugpy protocol)

- `DEBUGPY` unset/`0` → **`debugpy` is never imported** (verified by unit test).
- `DEBUGPY=1` → listener on `0.0.0.0:${DEBUGPY_PORT:-5678}`, **non-blocking**,
  app continues; IDE attaches on demand.
- Entry point: `app/core/debugging.py::configure_debugging()` called at the top
  of `app/main.py` module import — so `uv run uvicorn app.main:app`,
  `python -m scripts.…`, and tests all honor it.
- VS Code: `"type": "debugpy", "request": "attach", "connect": {"host": "localhost", "port": 5678}`.

---

## 9. Observability

- **App logs:** single-line `timestamp LEVEL logger :: message` on stdout;
  uvicorn access logs on. INFO by default (`BOR_LOG_LEVEL`).
- **Per-chat-turn log line (required):**
  `question=… embed_ms=… top_score=… fts_hits=… summary_hits=… tuning=N kb_chars=N threshold=… deflected=… sources=… thinking_chars=… tool_calls=N total_ms=…`
  (`thinking_chars=` counts the turn's reasoning chars — phase 17, owner
  permission 2026-08-23 — and is counted even when `BOR_STREAM_THINKING=0`
  suppresses the frames.)

> **Log-line revision (phase 37, owner permission 2026-08-26):** the
> required per-turn line gains `tool_calls=N` after `thinking_chars=` —
> the count of agent tool executions that consumed budget on the turn
> (phase 37's `list_documents` / `read_document`; rejected calls do not
> count, and deflected turns run no tools). `summary_hits=` (phase 30)
> and `kb_chars=` (phase 31) are recorded here as well; `sources=` lists
> the retrieval docs plus any agent-read documents, deduped.
- **Importer logs:** per-file `added|updated|unchanged|pruned` + summary
  (counts, embedding batches, total time).
- **`query_log` table:** durable record of every question (score, deflection,
  sources, latency) for tuning the threshold and finding gaps in the docs.

---

## 10. Testing Strategy (LOCKED — A16)

| Layer | Tooling | Runs | Gate |
|-------|---------|------|------|
| Unit | pytest | `uv run pytest tests/unit` | pass |
| Integration | pytest + FastAPI TestClient | `uv run pytest tests/integration` | pass |
| Coverage | pytest-cov on `app/` | `uv run pytest --cov=app --cov-report=term-missing` | **>90%** per phase |
| E2E | Playwright (sync API), one file per story | `uv run pytest tests/e2e/test_<story>.py -v --no-cov` | passes **in isolation** |

- **E2E determinism:** `tests/e2e/mock_llm.py` serves a deterministic
  OpenAI-compatible API. Embeddings are genuine L2-normalized token-overlap
  vectors, so the cosine threshold behaves like production: on-topic
  questions retrieve, off-topic questions deflect. `E2E_REAL_LLM=1` switches
  the app fixture to live aipi (needs imported KB).
- **E2E prerequisites:** `podman compose up -d db`; Chromium installed via
  `uv run playwright install chromium`.
- DB isolation: story E2E fixtures truncate `query_log` (and re-import
  fixtures for import-dependent stories) per test module.

---

## 11. Import & Update Workflow (documented in README)

```
# first import (and any future refresh):
uv run python -m scripts.import_docs                # defaults: ~/Homelab ~/Deployments
uv run python -m scripts.import_docs --source ~/OtherProject   # extra dirs
uv run python -m scripts.import_docs --prune        # drop deleted / filtered-out files
uv run python -m scripts.eval_retrieval "How did I install gitlab?"
uv run python -m scripts.llm_probe                  # sanity: models + dim
```
Behavior: sha256 delta per `(source, path)` — unchanged files are skipped
(no re-embedding); changed files are re-chunked + re-embedded (chunks
replaced atomically); `--prune` removes docs whose files disappeared or no
longer match the format filter. Formats per A9 (revised 2026-08-27):
`md, markdown, txt, yaml, yml, json, py`, the quadlet family
(`container, network, volume, image, pod, kube, swap, os, endpoint`), and
`j2` (plain-text chunked) (`BOR_IMPORT_EXTENSIONS`), hidden (dot)
directories skipped, exclusion list applied. `scripts/eval_retrieval.py`
ranks live hybrid results for a question (retrieval tuning).

---

## 12. Roadmap (one story → one phase → one Playwright gate)

| Phase | File | Story | Playwright gate |
|-------|------|-------|-----------------|
| 01 | `01_infrastructure.md` | — (foundation) | `tests/e2e/test_smoke.py` |
| 02 | `02_story_import_documents.md` | `import-documents.md` | `tests/e2e/test_import_documents.py` |
| 03 | `03_story_chat_rag.md` | `chat-rag-answer.md` | `tests/e2e/test_chat_rag.py` |
| 04 | `04_story_honest_deflection.md` | `honest-deflection.md` | `tests/e2e/test_honest_deflection.py` |
| 05 | `05_story_suggestion_chips.md` | `suggestion-chips.md` | `tests/e2e/test_suggestion_chips.py` |
| 06 | `06_story_loading_feedback.md` | `loading-feedback.md` | `tests/e2e/test_loading_feedback.py` |
| 07 | `07_story_responsive_polish.md` | `responsive-polish.md` | `tests/e2e/test_responsive_polish.py` |
| 08 | `08_story_dark_tech_theme.md` | `dark-tech-theme.md` | `tests/e2e/test_dark_tech_theme.py` |
| 09 | `09_story_retrieval_quality.md` | `retrieval-quality.md` | `tests/e2e/test_retrieval_quality.py` |
| 10 | `10_story_document_viewer.md` | `document-viewer.md` | `tests/e2e/test_document_viewer.py` |
| 17 | `17_thinking_display.md` | `thinking-display.md` | `tests/e2e/test_thinking_display.py` |
| 18 | `18_follow_bottom_scroll.md` | `follow-bottom-scroll.md` | `tests/e2e/test_follow_bottom_scroll.py` |
| 19 | `19_shared_header.md` | `shared-header.md` | `tests/e2e/test_shared_header.py` |
| 24 | `24_whole_document_context.md` | `whole-document-context.md` | `tests/e2e/test_whole_document_context.py` |

> Row 17 (thinking display) added 2026-08-23 with owner permission — the
> A15 SSE extension recorded in §4.
>
> Row 18 (follow-the-bottom scroll) added 2026-08-23 with owner choice —
> option 1: follow-the-bottom, no "↓ new content" pill (UI-behavior-only
> change; no anchor revised).
>
> Row 19 (shared header) added 2026-08-23 with owner permission —
> Sign in/Sign out + New Chat on every page via one shared module, and
> the phase-16 "Sources" link UX choice revised: the nav link is hidden
> for anonymous (the soft-gate page and the A10 API split are unchanged).
>
> Row 24 (whole-document context) added 2026-08-24 with owner permission
> — A7's 24k context cap removed (documents are never truncated)

Completion = unit+integration green, coverage >90%, story E2E green in
isolation, UI verification passed, **one `--no-gpg-sign` commit**.

---

## 13. Future (post-v1 hooks, deliberately not built)
- Auth (stateless API makes this a drop-in: sessions → Valkey).
- HNSW index on `chunks.embedding` at scale.
- Conversation persistence (messages tables).
- Watchdog auto-re-import (inotify) — until then the script is the truth.
- More sources: any directory of A9-format files via `--source`.