Refresh agent instruction files

.claude/rules/agents.md

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+## Kaizen Agents
+
+Specialized agent personas available on demand via the state-hub MCP.
+
+**Discover:** `list_kaizen_agents()` — returns all agents with name, description, category
+**Load:** `get_kaizen_agent("tdd-workflow")` — returns full instructions; read and follow them
+
+Common agents:
+
+| Agent | Category | When to use |
+|-------|----------|-------------|
+| `tdd-workflow` | testing | Step-by-step TDD8 workflow for any feature |
+| `code-refactoring` | quality | Code quality analysis and safe refactoring |
+| `test-maintenance` | testing | Diagnose and fix failing tests |
+| `requirements-engineering` | process | Prevent interface/mock mismatches upfront |
+| `keepaTodofile` | process | Maintain TODO.md during work |
+| `project-management` | process | Track status, determine next steps |
+| `datamodel-optimization` | quality | Optimize dataclasses and data structures |
+
+All 17 agents: call `list_kaizen_agents()` for the full list.

.claude/rules/architecture.md

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+## Architecture
+
+<!-- TODO: Describe the key design decisions and component structure.
+     Key modules, data flows, external integrations, state machines, etc. -->
+
+## Quick Reference
+
+`~/state-hub/mcp_server/TOOLS.md` — MCP tool reference

.claude/rules/first-session.md

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+## First Session Protocol
+
+Triggered when `get_domain_summary("markitect")` shows **no workstreams**.
+The project is registered but work has not yet been structured.
+
+**Step 1 — Read, don't write**
+- `~/the-custodian/canon/projects/markitect/project_charter_v0.1.md` — purpose, scope
+- `~/the-custodian/canon/projects/markitect/roadmap_v0.1.md` — planned phases
+- Scan repo root: README, directory structure, existing code or docs
+
+**Step 2 — Survey in-progress work**
+Look for TODOs, open branches, half-finished files. Note done vs. started but incomplete.
+
+**Step 3 — Propose workstreams to Bernd**
+Propose 1–3 workstreams — each a coherent strand, weeks to months, anchored to a
+roadmap phase. **Wait for approval before creating.**
+
+**Step 4 — Create workplan file first, then DB record (ADR-001)**
+```
+workplans/markitect-project-WP-NNNN-<slug>.md   ← write this first
+```
+Then register in the hub:
+```
+create_workstream(topic_id="5571d954-0d30-4950-980d-7bcaaad8e3e2", title="...", owner="...", description="...")
+create_task(workstream_id="<id>", title="...", priority="high|medium|low")
+```
+
+**Step 5 — Record the setup**
+```
+add_progress_event(
+    summary="First session: structured markitect into N workstreams, M tasks",
+    event_type="milestone",
+    topic_id="5571d954-0d30-4950-980d-7bcaaad8e3e2",
+    detail={"workstreams": [...], "tasks_created": M}
+)
+```
+
+<!-- Delete or archive this file once past first session -->

.claude/rules/repo-boundary.md

@@ -0,0 +1,8 @@
+## Repo boundary
+
+This repo owns **markitect-main** only. It does not own:
+
+<!-- TODO: List what belongs in adjacent repos, e.g.:
+- SSH key management → railiance-infra/
+- State hub code     → state-hub/
+-->

.claude/rules/repo-identity.md

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+**Purpose:** Knowledge artifact management system. Handles structured content creation, versioning, and publication workflows for the markitect domain.
+
+**Domain:** markitect
+**Repo slug:** markitect-project
+**Topic ID:** 5571d954-0d30-4950-980d-7bcaaad8e3e2

.claude/rules/session-protocol.md

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+## Session Protocol
+
+State Hub: http://127.0.0.1:8000
+
+**Step 1 — Orient**
+
+Read the offline-safe brief first — it works without a live hub connection:
+```bash
+cat .custodian-brief.md
+```
+Then call the MCP tool for richer cross-domain context when MCP tools are exposed:
+```
+get_domain_summary("markitect")
+```
+If MCP tools are unavailable in the current agent session, use the REST API:
+```bash
+curl -s "http://127.0.0.1:8000/state/summary" | python3 -m json.tool
+```
+If the hub is offline: `cd ~/state-hub && make api`
+
+**Step 2 — Check inbox**
+With MCP tools:
+```
+get_messages(to_agent="markitect-project", unread_only=True)
+```
+Mark read with `mark_message_read(message_id)`. Reply or act on coordination
+requests before proceeding.
+
+Without MCP tools:
+```bash
+curl -s "http://127.0.0.1:8000/messages/?to_agent=markitect-project&unread_only=true" \
+  | python3 -m json.tool
+curl -s -X PATCH "http://127.0.0.1:8000/messages/<id>/read" \
+  -H "Content-Type: application/json" -d '{}'
+```
+
+**Step 3 — Scan workplans**
+```bash
+ls workplans/
+```
+For each file with `status: ready`, `active`, or `blocked`, note pending
+`todo`/`in_progress` tasks.
+
+**Step 4 — Present brief**
+
+1. **Active workstreams** for `markitect` — title, task counts, blocking decisions
+2. **Pending tasks** from `workplans/` + any `[repo:markitect-project]` hub tasks
+3. **Goal guidance** — if `goal_guidance` in summary:
+   - `needs_workplan`: surface as top action — *"Repo goal '{title}' has no workplan yet"*
+   - `alignment_warnings`: flag if active work is not aligned with current goal
+4. **Suggested next action** — highest-priority open item
+5. **SBOM status** — flag if `last_sbom_at` is unset for this repo
+
+If no workstreams: follow First Session Protocol (`first-session.md`).
+
+**During work:** `record_decision()` · `add_progress_event()` · `resolve_decision()`
+
+> State Hub is a *read model*. Bootstrap tools (`create_workstream`, `create_task`)
+> are First Session Protocol only. Work structure belongs in repo files (ADR-001).
+
+**Session close:**
+With MCP tools:
+```
+add_progress_event(summary="...", topic_id="5571d954-0d30-4950-980d-7bcaaad8e3e2", workstream_id="<uuid>")
+```
+Without MCP tools:
+```bash
+curl -s -X POST http://127.0.0.1:8000/progress/ \
+  -H "Content-Type: application/json" \
+  -d '{"topic_id":"5571d954-0d30-4950-980d-7bcaaad8e3e2","workstream_id":"<uuid>","event_type":"note","summary":"what changed","author":"codex"}'
+```
+If workplan files were modified, ensure the local copy is up to date first:
+```bash
+git -C <repo_path> pull --ff-only
+cd ~/state-hub && make fix-consistency REPO=markitect-project
+```
+For repos where implementation runs on a remote machine (e.g. CoulombCore),
+use the combined target which pulls before fixing:
+```bash
+cd ~/state-hub && make fix-consistency-remote REPO=markitect-project
+```
+**C-15** (DB task ahead of file) is normal in multi-machine workflows — writeback
+will sync the file to match DB.  **C-16** (repo behind remote) blocks all writes
+until you pull — intentional to prevent clobbering remote progress.

.claude/rules/stack-and-commands.md

@@ -0,0 +1,19 @@
+## Stack
+
+<!-- TODO: Fill in language, frameworks, and key dependencies -->
+- **Language:**
+- **Key deps:**
+
+## Dev Commands
+
+```bash
+# TODO: Fill in the standard commands for this repo
+
+# Install dependencies
+
+# Run tests
+
+# Lint / type check
+
+# Build / package (if applicable)
+```

.claude/rules/workplan-convention.md

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+## Workplan Convention (ADR-001)
+
+File location: `workplans/markitect-project-WP-NNNN-<slug>.md`
+ID prefix: `MARKITECT-WP`
+
+Work items originate as files in this repo **before** being registered in the hub.
+
+Canonical workplan/workstream frontmatter statuses are:
+`proposed`, `ready`, `active`, `blocked`, `backlog`, `finished`, `archived`.
+Use `proposed` for a newly drafted plan, `ready` after review against current
+repo state, and `finished` when implementation is complete. `stalled` and
+`needs_review` are derived health labels, not stored statuses.
+
+Closed workplans may be moved to `workplans/archived/` with a completion-date
+prefix: `YYMMDD-markitect-project-WP-NNNN-<slug>.md`. The frontmatter id remains
+unchanged; the prefix is only for quick visual reference.
+
+Small opportunistic tasks discovered during another session use **Ad Hoc Tasks**:
+`workplans/ADHOC-YYYY-MM-DD.md`, workstream slug `adhoc-YYYY-MM-DD`, and task ids
+`ADHOC-YYYY-MM-DD-T01`, `T02`, etc. Use adhocs only for low-risk work completed
+directly. Promote anything requiring analysis, design, approval, dependencies, or
+multiple planned phases into a normal workplan.
+
+Ecosystem todos from other agents arrive as `[repo:markitect-project]` hub tasks —
+visible at session start. Pick one up by creating the workplan file, then registering
+the workstream.
+
+<!-- Ralph Loop rules and HEUREKA sequence: ~/.claude/CLAUDE.md — do not duplicate here -->

AGENTS.md

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+# markitect-main — Agent Instructions
+
+## Repo Identity
+
+**Purpose:** Knowledge artifact management system. Handles structured content creation, versioning, and publication workflows for the markitect domain.
+
+**Domain:** markitect
+**Repo slug:** markitect-project
+**Topic ID:** `5571d954-0d30-4950-980d-7bcaaad8e3e2`
+**Workplan prefix:** `MARKITECT-WP-`
+
+---
+
+## State Hub Integration
+
+The Custodian State Hub tracks work across all domains. Interact via HTTP REST —
+there is no MCP server for Codex agents.
+
+| Context | URL |
+|---------|-----|
+| Local workstation | `http://127.0.0.1:8000` |
+| Remote via tunnel | `http://127.0.0.1:18000` |
+
+### Orient at session start
+
+```bash
+# Offline brief — works without hub connection
+cat .custodian-brief.md
+
+# Active workstreams for this domain
+curl -s "http://127.0.0.1:8000/workstreams/?topic_id=5571d954-0d30-4950-980d-7bcaaad8e3e2&status=active" \
+  | python3 -m json.tool
+
+# Check inbox
+curl -s "http://127.0.0.1:8000/messages/?to_agent=markitect-project&unread_only=true" \
+  | python3 -m json.tool
+```
+
+Mark a message read:
+```bash
+curl -s -X PATCH "http://127.0.0.1:8000/messages/<id>/read" \
+  -H "Content-Type: application/json" -d '{}'
+```
+
+### Log progress (required at session close)
+
+```bash
+curl -s -X POST http://127.0.0.1:8000/progress/ \
+  -H "Content-Type: application/json" \
+  -d '{
+    "summary": "what was done",
+    "event_type": "note",
+    "author": "codex",
+    "workstream_id": "<uuid>",
+    "task_id": "<uuid>"
+  }'
+```
+
+Omit `workstream_id` / `task_id` when not applicable.
+
+### Update task status
+
+```bash
+curl -s -X PATCH "http://127.0.0.1:8000/tasks/<task_id>" \
+  -H "Content-Type: application/json" \
+  -d '{"status": "in_progress"}'
+# values: todo | in_progress | done | blocked
+```
+
+### Flag a task for human review
+
+```bash
+curl -s -X PATCH "http://127.0.0.1:8000/tasks/<task_id>" \
+  -H "Content-Type: application/json" \
+  -d '{"needs_human": true, "intervention_note": "reason"}'
+```
+
+---
+
+## Session Protocol
+
+**Start:**
+1. `cat .custodian-brief.md` — domain goal and open workstreams (offline-safe)
+2. Check inbox: `GET /messages/?to_agent=markitect-project&unread_only=true`; mark read
+3. Scan workplans: `ls workplans/` — note `status: ready`, `active`, or `blocked` files and open tasks
+4. Check blocked tasks: `GET /tasks/?needs_human=true`
+
+**During work:**
+- Update task statuses in workplan files as tasks progress
+- Record significant decisions via `POST /decisions/`
+
+**Close:**
+1. Update workplan file task statuses to reflect progress
+2. Log: `POST /progress/` with a summary of what changed
+3. Note for the custodian operator: after workplan file changes, run from
+   `~/state-hub`:
+   ```bash
+   make fix-consistency REPO=markitect-project
+   ```
+   This syncs task status from files into the hub DB.
+
+---
+
+## Workplan Convention (ADR-001)
+
+Work items originate as files in this repo — not in the hub. The hub is a
+read/cache/index layer that rebuilds from files.
+
+**File location:** `workplans/MARKITECT-WP-NNNN-<slug>.md`
+
+**Archived location:** finished workplans may move to
+`workplans/archived/YYMMDD-MARKITECT-WP-NNNN-<slug>.md`. The `YYMMDD` prefix is
+the completion/archive date; the frontmatter `id` does not change.
+
+**Ad Hoc Tasks:** small opportunistic fixes discovered during a session use
+`workplans/ADHOC-YYYY-MM-DD.md` with task ids `ADHOC-YYYY-MM-DD-T01`, etc. Use
+this only for low-risk work completed directly; create a normal workplan for
+anything needing analysis, design, approval, dependencies, or multiple phases.
+
+**Frontmatter:**
+
+```yaml
+---
+id: MARKITECT-WP-NNNN
+type: workplan
+title: "..."
+domain: markitect
+repo: markitect-project
+status: proposed | ready | active | blocked | backlog | finished | archived
+owner: codex
+topic_slug: ...
+created: "YYYY-MM-DD"
+updated: "YYYY-MM-DD"
+state_hub_workstream_id: "<uuid>"   # written by fix-consistency — do not edit
+---
+```
+
+Use `proposed` for a new draft, `ready` after review against current repo
+state, and `finished` after implementation. `stalled` and `needs_review` are
+derived health labels, not frontmatter statuses.
+
+**Task block format** (one per `##` section):
+
+```
+## Task Title
+
+` ` `task
+id: MARKITECT-WP-NNNN-T01
+status: todo | in_progress | done | blocked
+priority: high | medium | low
+state_hub_task_id: "<uuid>"         # written by fix-consistency — do not edit
+` ` `
+
+Task description text.
+```
+
+Status progression: `todo` → `in_progress` → `done` (or `blocked`)
+
+To create a new workplan:
+1. Write the file following the format above
+2. Notify the custodian operator to run `make fix-consistency REPO=markitect-project`
+   (or send a message to the hub agent via `POST /messages/`)

CLAUDE.md

@@ -1,120 +1,11 @@
-# CLAUDE.md
+# markitect-main — Claude Code Instructions
-
+
-This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+@SCOPE.md
-
+@.claude/rules/repo-identity.md
-## Custodian State Hub Integration
+@.claude/rules/session-protocol.md
-
+@.claude/rules/first-session.md
-This project is tracked as the **markitect** domain in the Custodian State Hub.
+@.claude/rules/workplan-convention.md
-Hub topic ID: `5571d954-0d30-4950-980d-7bcaaad8e3e2`
+@.claude/rules/stack-and-commands.md
-
+@.claude/rules/architecture.md
-**Session start:** Call `get_domain_summary("markitect")` via the `state-hub` MCP tool.
+@.claude/rules/repo-boundary.md
-If the hub is not reachable: `cd ~/the-custodian/state-hub && make api`
+@.claude/rules/agents.md
-
-**Session end:** Call `add_progress_event()` with `topic_id` above, a `summary`, and `event_type` (`note` / `milestone` / `blocker`).
-
-**Available state-hub MCP tools:** `get_state_summary`, `get_domain_summary`, `add_progress_event`, `create_workstream`, `create_task`, `update_task_status`, `record_decision`, `resolve_decision`.
-
-If the hub API is unavailable, use `curl` against `http://127.0.0.1:8000/docs`.
-
----
-
-## Development Commands
-
-All commands assume the `markitect-venv` virtual environment is active (`source ~/.venvs/markitect-venv/bin/activate` or equivalent). The package is installed in editable mode.
-
-```bash
-# Run the core test suite
-pytest
-
-# Run a single test file
-pytest tests/test_issue_17_batch_processing.py
-
-# Run tests by marker
-pytest -m unit
-pytest -m "not slow"
-
-# Run with coverage
-pytest --cov=markitect
-
-# Run only fast unit tests (TDD inner loop)
-pytest tests/unit/
-
-# CLI entry point
-markitect --help
-
-# Infospace subcommands (primary active development area)
-markitect infospace --help
-markitect infospace eval-summary --update-metrics
-
-# LLM helper commands
-markitect llm-helper "<question>"
-markitect llm-catalog
-markitect llm-check
-markitect llm-default
-markitect llm-preference
-
-# Install / reinstall in dev mode
-pip install -e ".[analysis]"
-```
-
-## Architecture
-
-MarkiTect is a CLI-driven markdown engine that treats documents as structured, queryable information spaces. Entry point: `markitect/cli.py` → `main()` (Click group). All subcommand groups are registered at the bottom of `cli.py`.
-
-### Core Modules (`markitect/`)
-
-| Module | Purpose |
-|--------|---------|
-| `spaces/` | InformationSpace model — composability, events, history, transclusion, rendering, sync |
-| `prompts/` | Prompt resolver, compiler, execution engine, quality gates, dependency graph, traceability |
-| `llm/` | LLM adapter layer — 4 text providers + embedding adapter; 7-layer config resolution |
-| `infospace/` | Infospace lifecycle — init, entity parsing, evaluation, composition, graph export |
-| `analysis/` | Graph analysis (networkx) and FCA (Formal Concept Analysis, pure Python) |
-| `schema*/` | Schema generation, validation, naming, refinement, metaschema |
-| `core/` | Foundational parser, AST, serializer, workspace |
-
-### LLM Configuration (`markitect/llm/`)
-
-Resolution order (highest → lowest priority):
-1. CLI flags (`--provider`, `--model`)
-2. `MARKITECT_HELPER_MODEL` env var (model only)
-3. User preference (`[llm.preference]` in `~/.config/markitect/config.toml`)
-4. Directory preference (`[llm.preference]` in `.markitect.toml`)
-5. Directory default (`[llm.default]` in `.markitect.toml`)
-6. User default (`[llm.default]` in `~/.config/markitect/config.toml`)
-7. Hardcoded fallback: `gemini/gemini-2.5-flash`
-
-Canonical models: `markitect/llm/models.py` (`RunConfig`, `LLMResponse`) and `markitect/llm/adapter.py` (`LLMAdapter`). These are mirrored in the standalone `/home/worsch/llm-connect/` package (`llm_connect`), which is installed as a local path dependency. `markitect/prompts/execution/{models,llm_adapter}.py` are re-export shims for backward compatibility.
-
-**Gotcha:** The `OPENROUTER_API_KEY` env var may hold a stale key — `unset OPENROUTER_API_KEY` before running LLM commands if you get auth errors. `claude-code` provider fails inside Claude Code sessions (nested session restriction).
-
-### Infospace (`markitect/infospace/`)
-
-An infospace is a directory-based collection of typed entities governed by an `infospace.yaml` config. Key files:
-- `config.py` — config loading, `find_infospace_config()`, `DisciplineBinding`
-- `entity_parser.py` — parse entity markdown files from `output/entities/<slug>.md`
-- `evaluation.py` / `evaluation_io.py` — per-entity LLM evaluation (5 dimensions)
-- `state.py` — `build_state()` aggregates entity + evaluation state
-- `history.py` / `checks/` — viability tracking and collection-level checks
-
-Slugs use **underscores** (e.g., `accumulation_of_stock`). Active example: `examples/infospace-with-history/` (988 entities).
-
-### Layered Architecture
-
-The project has a partially-implemented layered architecture separate from `markitect/`:
-- `domain/` — domain models (issues, projects)
-- `infrastructure/` — config, repositories, logging, connection management
-- `application/` — application layer (mostly empty)
-- `capabilities/` — pluggable capability packages (`issue-facade`, `release-management`, `testdrive-jsui`, `markitect-utils`, `markitect-content`, `kaizen-agentic`)
-
-### Tests
-
-Tests live in `tests/`. Many test files are named `test_issue_NNN_*.py` (TDD by issue). Layered tests follow `test_l{N}_*.py` naming. The `tests/unit/` subtree has the cleanest structure and covers `prompts/`, `spaces/`, `llm/`, `infospace/`, `analysis/`.
-
-Pytest config is in `pytest.ini`. Relevant markers: `unit`, `integration`, `e2e`, `slow`, `performance`.
-
-### Active Roadmap Files
-
-- `roadmap/infospace-tooling/PLAN.md` — main infospace roadmap (S1 ✅ S2 ✅ S3 nearly done)
-- `roadmap/infospace-s3-closeout/PLAN.md` — S3 close-out tasks (C.1–C.8)
-- `roadmap/llm-shared-library/PLAN.md` — llm-connect extraction (S1+S2 done, S3 pending)