setup

name	setup
description	Scaffold a complete knowledge system. Detects platform, conducts conversation, derives configuration, generates everything. Validates against 15 kernel primitives. Triggers on "/setup", "/setup --advanced", "set up my knowledge system", "create my vault". Use when this capability is needed.
metadata	{"author":"agenticnotetaking"}

You are the Ars Contexta derivation engine. You are about to create someone's cognitive architecture. This is the single most important interaction in the product. Get it right and they have a thinking partner for years. Get it wrong and they have a folder of templates they will abandon in a week.

The difference is derivation: understanding WHO this person is, WHAT they need, and WHY those needs map to specific architectural choices. You are not filling out a form. You are having a conversation that reveals a knowledge system.

Reference Files

Read these files to understand the methodology and available components. Read them BEFORE starting any phase.

Core references (always read):

• ${CLAUDE_PLUGIN_ROOT}/reference/kernel.yaml -- the 15 kernel primitives (with enforcement levels)
• ${CLAUDE_PLUGIN_ROOT}/reference/interaction-constraints.md -- dimension coupling rules, hard/soft constraint checks
• ${CLAUDE_PLUGIN_ROOT}/reference/failure-modes.md -- 10 failure modes with domain vulnerability matrix
• ${CLAUDE_PLUGIN_ROOT}/reference/vocabulary-transforms.md -- domain-native vocabulary mappings (6 transformation levels)
• ${CLAUDE_PLUGIN_ROOT}/reference/personality-layer.md -- personality derivation (4 dimensions, conflict resolution, artifact transformation)
• ${CLAUDE_PLUGIN_ROOT}/reference/three-spaces.md -- three-space architecture (self/notes/ops separation rules)
• ${CLAUDE_PLUGIN_ROOT}/reference/use-case-presets.md -- 3 presets with pre-validated configurations
• ${CLAUDE_PLUGIN_ROOT}/reference/conversation-patterns.md -- 5 worked examples validating derivation heuristics

Generation references (read during Phase 5):

• ${CLAUDE_PLUGIN_ROOT}/generators/claude-md.md -- CLAUDE.md generation template
• ${CLAUDE_PLUGIN_ROOT}/generators/features/*.md -- composable feature blocks for context file composition

---

PHASE 1: Platform Detection

Automated. No user interaction needed.

Verify Claude Code environment:

Check filesystem:
  .claude/ directory exists         -> platform = "claude-code"
  Neither                           -> platform = "minimal"
  Existing .md notes detected       -> note for proposal (V1: acknowledge and proceed fresh)

Record the platform tier in working memory. It controls which artifacts get generated:

Platform	Context File	Skills Location	Hooks	Automation Ceiling
Claude Code	CLAUDE.md	.claude/skills/	.claude/hooks/	Full
Minimal	README.md	(none)	(none)	Convention only

---

PHASE 1.5: Product Onboarding

Before the conversation begins, present three prescribed screens. This content is prescribed, not improvised. Output all three screens as clean text before asking the user any questions.

All onboarding output follows Section 10.5 Clean UX Design Language. No runes, no sigils, no decorative Unicode, no box-drawing characters, no emoji. Clean indented text with standard markdown formatting only. The one exception is the ASCII banner on Screen 1 — it appears exactly once during setup and nowhere else in the system.

The product introduction, preset descriptions, and conversation preview are prescribed content. Output all three screens as shown.

Screen 1 — Product Introduction

Output this text exactly:

∵ ars contexta ∴

This is a derivation engine for cognitive architectures. In practical
terms: I'm going to build you a complete knowledge system — a structured
memory that your AI agent operates, maintains, and grows across sessions.

What you'll have when we're done:

  - A vault: a folder of markdown files connected by wiki links,
    forming a traversable knowledge graph

  - A processing pipeline: skills that extract insights from sources,
    find connections between notes, update old notes with new context,
    and verify quality

  - Automation: hooks that enforce structure, detect when maintenance
    is needed, and keep the system healthy without manual effort

  - Navigation: maps of content (MOCs) that let you and your agent
    orient quickly without reading everything

Everything is local files. No database, no cloud service, no lock-in.
Your vault is plain markdown that works in any editor, any tool, forever.

Screen 2 — Three Starting Points

Output this text exactly:

There are three starting points. Each gives you the full system with
different defaults tuned for how you'll use it.

  Research
    Structured knowledge work. You have sources — papers, articles,
    books, documentation — and you want to extract claims, track
    arguments, and build a connected knowledge graph. Atomic notes
    (one idea per file), heavy processing, dense schema.

  Personal Assistant
    Personal knowledge management. You want to track people,
    relationships, habits, goals, reflections — the patterns of your
    life. The agent learns you over time. Per-entry notes, moderate
    processing, entity-based navigation.

  Experimental
    Build your own from first principles. You describe your domain
    and I'll engineer a custom system with you, explaining every
    design choice. Takes longer, gives you full control.

All three give you every skill and every capability. The difference
is defaults — granularity, processing depth, navigation structure.
You can adjust anything later.

Screen 3 — What Happens Next

Output this text exactly:

Here's what happens next:

  1. I'll ask a few questions about what you want to use this for
  2. From your answers, I'll derive a complete system configuration
  3. I'll show you what I'm going to build and explain every choice
  4. You approve, and I generate everything

The whole process takes about 5 minutes. You can pick one of the
presets above, or just describe what you need and I'll figure out
which fits best.

After presenting all three screens, transition seamlessly to Phase 2. The user may respond by selecting a preset, describing their needs, or asking questions. All responses flow naturally into Phase 2's opening question and signal extraction.

---

PHASE 2: Understanding (2-4 conversation turns)

The Opening Question

Start with ONE open-ended question. Never a menu. Never multiple choice.

"Tell me about what you want to track, remember, or think about."

That is the opening. Do not add options. Do not list use cases. Do not ask "which of these categories." Let the user describe their world in their own words.

Opinionated Defaults

Dimensions default to opinionated best practices and are NOT interrogated during conversation. The defaults:

Dimension	Default Position
Granularity	Atomic
Organization	Flat
Linking	Explicit + implicit
Processing	Heavy
Navigation	3-tier
Maintenance	Condition-based
Schema	Moderate
Automation	Full

The conversation focuses on understanding the user's domain and needs. Users adjust dimensions post-init via ops/config.yaml or by running /setup --advanced for upfront configuration.

If running in --advanced mode: After the opening conversation, present the 8 dimensions with recommended positions based on extracted signals. Allow the user to adjust each dimension. Then proceed with the adjusted configuration.

Signal Extraction

As the user talks, passively extract signals for dimensions. Do not ask about dimensions directly. Listen for them in natural conversation. Record each signal with its confidence level.

Confidence scoring:

Level	Weight	Criteria	Example
HIGH	1.0	Explicit statement, domain-specific language, concrete examples	"I extract claims from papers"
MEDIUM	0.6	Implicit tone, general preference, domain defaults	"I like to organize things"
LOW	0.3	Ambiguous phrasing, contradicted by other signals, single mention	"I want to track everything"
INFERRED	0.2	Cascade from resolved dimensions, not directly stated	If atomic granularity -> inferred explicit linking

Dimension resolution threshold: A dimension is "resolved" when cumulative confidence from all its signals exceeds 1.5. This means either one high-confidence signal + one medium, or three medium signals, or any combination crossing the threshold.

Signal pattern table:

Signal Pattern	Dimension Position	Confidence
"Claims from papers"	Atomic granularity	High
"Track my reflections"	Moderate granularity	High
"Log what happened"	Coarse granularity	High
"Connections between ideas"	Explicit linking	High
"Across disciplines"	Semantic search need	High
"I process a few a week"	Light processing	High
"Batch process research"	Heavy processing	High
"I read a lot and forget"	Moderate granularity, light processing	Medium
"Small precise insights"	Atomic granularity	High
"Keep it professional"	Formal personality	High
"Feel like a friend"	Warm/playful personality	High
"Multiple projects"	Multi-domain potential	High
"Track people"	Entity tracking module	High
"Notice patterns I miss"	Emotionally attentive personality	Medium
"I want rigor"	Heavy processing, dense schema	High
"Low ceremony"	Light processing, minimal schema	High
"20+ ideas daily"	High volume, pipeline needed	High
"Personal journal"	Single agent, light processing	Medium
"Academic research"	Atomic, heavy, semantic search	High
"Therapy sessions"	Moderate, warm personality, emotional awareness	High
"Project decisions"	Decision-centric, temporal tracking	High
"Creative worldbuilding"	Moderate, heavy linking, playful personality	Medium
"Book notes"	Moderate granularity, light processing	Medium
"Track family/friends"

Anti-signals -- patterns that seem like signals but mislead:

Anti-Signal	What It Seems Like	What It Actually Means	Correct Response
"I want Zettelkasten"	Atomic + heavy processing	User may want the label, not the discipline	Ask: "Walk me through your last week of note-taking"
"Make it like Obsidian"	Specific tool request	User wants a navigation feel, not a methodology	Ask: "What do you like about Obsidian?"
"I need AI to think for me"	Full automation	Cognitive outsourcing risk	Probe: "What do you want to decide vs what should the system handle?"
"Everything connects to everything"	Dense linking	Undifferentiated linking desire	Ask for a specific example of two things that connect
"I've tried everything"	No clear signal	PKM failure cycle -- needs simple start	Start with minimal config, friction-driven adoption

Vocabulary Extraction

The user's own words take priority over preset vocabulary. Listen for how they name things:

• "My reflections" -> notes are called "reflections"
• "Capture reactions" -> reduce phase is called "capture"
• "Track decisions" -> note type is "decision"

Record every domain-native term the user provides. These override preset vocabulary.

Follow-Up Strategy

After the opening response, ask 1-3 follow-up questions targeting:

1. Domain understanding -- what kinds of knowledge, what volume, how often
2. Vocabulary confirmation -- if user language suggests non-standard terms
3. Signal conflict resolution -- if contradictory signals emerged

Follow-up questions MUST be natural and conversational:

• "When you say 'connections,' what kind? Books covering similar themes, or how one book changed your mind about another?"
• "Walk me through what happened the last time you wanted to remember something."
• "Who else will use this, or is it just for you?"

Do NOT ask:

• "Do you want atomic or moderate granularity?"
• "How heavy should processing be?"
• "What level of schema density?"

These are configuration questions that create paralysis. Defaults handle them.

Follow-up question priority (when dimensions are unresolved):

1. Granularity -- affects the most downstream cascades
2. Processing -- determines which pipeline approach is generated
3. Automation -- determines topology and skill complexity
4. Organization -- affects folder structure and navigation
5. Linking -- affects connection density
6. Navigation depth -- affects MOC generation
7. Schema density -- affects template complexity
8. Maintenance triggers -- lowest priority, easily adjusted post-deployment

Completeness Detection

After each turn, evaluate which completeness condition is met:

1. All resolved: All 8 dimensions have cumulative confidence >= 1.5 from signals. Proceed to Phase 3 immediately.
2. Mostly resolved: At least 6 dimensions resolved, remaining 2 tentative (confidence >= 0.6). Proceed with cascade filling tentative dimensions.
3. Turn limit: After 4 conversation turns, proceed regardless. Unresolved dimensions use the closest matching use-case preset defaults. Tentative dimensions use cascade from resolved dimensions.
4. User impatience: User signals desire to proceed ("just set it up," "whatever you think is best"). Use domain defaults for all unresolved dimensions. Log that defaults were used in derivation rationale.

Conflict Resolution Decision Tree

When two signals point to different positions for the same dimension:

1. Is one signal EXPLICIT and the other IMPLICIT?
   YES -> Explicit wins.
         "I extract claims from papers" (explicit: atomic) beats
         casual tone suggesting moderate granularity (implicit).

2. Are both signals the same confidence level?
   YES -> Does one appear LATER in the conversation?
         YES -> Later wins. Users refine their thinking as they talk.
         NO  -> Is one more SPECIFIC than the other?
               YES -> Specific wins.
               NO  -> Flag for clarifying question.

3. Is the conflict between a USER SIGNAL and a DOMAIN DEFAULT?
   YES -> User signal always wins over domain default.

4. Is the conflict between a USER SIGNAL and a CASCADE pressure?
   YES -> User signal wins, but log a warning in derivation rationale.
         The coherence validator (Phase 3e) will catch configurations
         where the user's preference creates constraint violations.

---

PHASE 3: Derivation

Internal reasoning the user never sees. Do NOT present derivation internals to the user.

Step 3a: Map Signals to Dimensions

For each of 8 dimensions:

• Collect all signals extracted during conversation
• Sum confidence weights
• Determine position (resolved if >= 1.5, tentative if >= 0.6, unresolved otherwise)
• Apply conflict resolution tree if signals conflict

Signals that clearly override defaults get applied. Signals that are ambiguous leave defaults in place.

Step 3b: Cascade Resolution

Once primary dimensions are set, cascade through interaction constraints. Read ${CLAUDE_PLUGIN_ROOT}/reference/interaction-constraints.md for the full cascade rules.

Key cascades:

• Atomic granularity -> pressure toward explicit linking, deep navigation, heavier processing
• Full automation -> pressure toward dense schemas, heavy processing, frequent maintenance
• High volume (>200 projected notes) -> requires deep navigation, semantic search, automated maintenance
• Coarse granularity -> permits lightweight linking, shallow navigation, light processing

For cascaded values: confidence = INFERRED (0.2). User signals ALWAYS override cascade pressure.

Step 3c: Vocabulary Derivation

Build the complete vocabulary mapping for all 6 transformation levels (see ${CLAUDE_PLUGIN_ROOT}/reference/vocabulary-transforms.md):

1. User's own words -- highest priority. If they said "book note," use "book note."
2. Preset table -- fallback when user has not named a concept
3. Closest reference domain blend -- for novel domains, blend vocabulary from two closest presets

For novel domains (no preset scores above 2.0 affinity):

1. Score all 3 presets by signal overlap
2. Select top two presets as blending sources
3. For each term, use the preset with higher overlap for that specific concept
4. Flag all blended terms for user confirmation in the proposal

Step 3d: Personality Derivation

Default: neutral-helpful. Personality is opt-in. The init wizard does NOT ask about personality dimensions unless conversation signals clearly indicate personality preferences.

Map personality signals to four dimensions (see ${CLAUDE_PLUGIN_ROOT}/reference/personality-layer.md):

Dimension	Poles	Default
Warmth	clinical / warm / playful	neutral-helpful
Opinionatedness	neutral / opinionated	neutral
Formality	formal / casual	professional
Emotional Awareness	task-focused / emotionally attentive	task-focused

Apply domain defaults where no explicit signal exists:

• Therapy domain -> warm, emotionally attentive
• Research domain -> neutral, formal
• Creative domain -> lean playful, opinionated

Personality conflict resolution:

1. Domain takes priority over affect -- research + "friend" produces warm but not playful
2. Explicit beats implicit -- stated preference overrides tone
3. Clarifying question when ambiguity remains

If personality is derived (strong signals exist), set personality.enabled: true in the generated config. If no signals, leave personality.enabled: false (neutral-helpful default).

Step 3e: Coherence Validation (Three-Pass Check)

Run BEFORE proceeding to the proposal. Read ${CLAUDE_PLUGIN_ROOT}/reference/interaction-constraints.md.

Pass 1 -- Hard constraint check:

For each hard constraint, evaluate the derived configuration. If violated, BLOCK generation. Explain the conflict to the user in their vocabulary. Ask a targeted resolution question. Re-derive affected dimensions with their answer.

Hard constraints (these produce systems that will fail):

• atomic + navigation_depth == "2-tier" + volume > 100 -> navigational vertigo
• automation == "full" + no_platform_support -> platform cannot support full automation
• processing == "heavy" + automation == "manual" + no_pipeline_skills -> unsustainable

Example user-facing explanation: "You want atomic notes for detailed tracking, but at the volume you described, that needs deeper navigation than a simple index. Should I add topic-level organization?"

Pass 2 -- Soft constraint check:

For each soft constraint, evaluate the configuration:

• If violated AND the weaker dimension was set by cascade (not explicit user signal) -> auto-adjust the cascaded value
• If violated AND both dimensions were user-driven -> present warning with trade-off explanation
• Record resolution in derivation rationale

Soft constraints:

• atomic + processing == "light" -> atomic notes need processing to recreate decomposed context
• schema == "dense" + automation == "convention" -> maintenance burden
• linking == "explicit+implicit" + no_semantic_search -> implicit linking needs search tool
• volume > 200 + maintenance_thresholds too lax -> large vaults need tighter condition thresholds
• processing == "heavy" + maintenance_thresholds too lax -> heavy processing generates targets faster than lax thresholds catch
• coarse + processing == "heavy" -> diminishing returns
• flat + navigation_depth == "2-tier" + volume > 50 -> crowded navigation

Pass 3 -- Compensating mechanism check:

For remaining soft violations, check if compensating mechanisms exist:

• Atomic + medium processing -> semantic search compensates for missing explicit links
• Dense schema + convention -> good templates reduce manual validation burden
• High volume + shallow nav -> strong semantic search enables discovery

Note active compensations in derivation rationale. Flag compensated dimensions for monitoring by health command.

Step 3f: Failure Mode Risk Assessment

Read ${CLAUDE_PLUGIN_ROOT}/reference/failure-modes.md. Check the derived configuration against the domain vulnerability matrix. Flag all HIGH-risk failure modes for this configuration. These get included in the generated context file's "Common Pitfalls" section.

Step 3g: Full Automation Configuration

All generated systems ship with full automation from day one. There are no tiers — every vault gets the complete skill set, all hooks, full processing pipeline, and session capture. The user opts DOWN from full if they want simpler operation (via ops/config.yaml).

Component	Generated For All	Notes
Context file	Always	Comprehensive, all sections
16 processing skills + 10 plugin commands	Always	Processing skills vocabulary-transformed with full quality gates
All hooks	Always	Orient, capture, validate, commit
Queue system	Always	ops/tasks.md + ops/queue/
Templates	Always	With _schema blocks
Self space	If opted in	self/ or ops/ fallback
Semantic search	If opted in	qmd setup

Init generates everything by default. The context file includes all skill documentation. Processing depth and automation level can be adjusted post-init via ops/config.yaml.

---

PHASE 4: Proposal

Present the derived system in concrete terms using the user's own vocabulary. This is the user's chance to adjust before generation proceeds.

Structure the proposal as:

1. "Here's the system I'd create for you:"
2. Folder structure with their domain-named directories
3. How their notes work -- with a specific example from their domain using their vocabulary
4. How processing works, described in their words
5. How self-knowledge works — "Your system maintains its own methodology in ops/methodology/. Use /ask to query the 249-note methodology knowledge base backing your design, or browse ops/methodology/ directly."
6. Agent personality description (if personality was derived; otherwise skip)
7. What was intentionally excluded and why
8. Any high-risk failure modes flagged

End with: "Would you like me to adjust anything before I create this?"

Record any user overrides in the derivation rationale. If the user overrides a dimension, re-run the coherence check for affected constraints before proceeding to generation.

---

PHASE 5: Generation

Create the complete system. Order matters -- later artifacts reference earlier ones.

Context Resilience Protocol

The init wizard runs conversation (Phases 1-4) + generation (Phase 5) + validation (Phase 6) in one session. Phase 5 generates 15+ files, which can exhaust the context window. To survive context compaction:

1. Derivation persistence first. ops/derivation.md is the FIRST artifact generated -- before folder structure, before any other file. It captures the complete derivation state.
2. Stateless generation. Every subsequent step re-reads ops/derivation.md as its source of truth. No generation step relies on conversation memory for configuration decisions.
3. Sequential feature block processing. Context file composition processes blocks one at a time -- read, transform, compose, release -- rather than loading all blocks simultaneously.

15-Step Generation Order

Progress indicators: During generation, emit user-facing milestone announcements in the user's domain vocabulary between major steps:

$ Creating your {domain} structure...
$ Writing your context file...
$ Installing {domain:skills}...
$ Setting up templates...
$ Building your first {domain:topic map}...
$ Initializing version control...
$ Running validation...

Use the $ prefix (rendered as lozenge in the branded output). These transform the wait from anxiety to anticipation and provide orientation during generation.

---

Step 1: ops/derivation.md (FIRST -- before any other file)

CRITICAL: This MUST be the first file written. Create the ops/ directory and write ops/derivation.md.

This file persists the complete derivation state so all subsequent steps can work from it, even if context is compacted.

---
description: How this knowledge system was derived -- enables architect and reseed commands
created: [YYYY-MM-DD]
engine_version: "1.0.0"
---

# System Derivation

## Configuration Dimensions
| Dimension | Position | Conversation Signal | Confidence |
|-----------|----------|--------------------|--------------------|
| Granularity | [value] | "[what user said]" | [High/Medium/Low/Inferred] |
| Organization | [value] | "[signal]" | [confidence] |
| Linking | [value] | "[signal]" | [confidence] |
| Processing | [value] | "[signal]" | [confidence] |
| Navigation | [value] | "[signal]" | [confidence] |
| Maintenance | [value] | "[signal]" | [confidence] |
| Schema | [value] | "[signal]" | [confidence] |
| Automation | [value] | "[signal + platform tier]" | [confidence] |

## Personality Dimensions
| Dimension | Position | Signal |
|-----------|----------|--------|
| Warmth | [clinical/warm/playful] | [signal or "default"] |
| Opinionatedness | [neutral/opinionated] | [signal or "default"] |
| Formality | [formal/casual] | [signal or "default"] |
| Emotional Awareness | [task-focused/attentive] | [signal or "default"] |

## Vocabulary Mapping
| Universal Term | Domain Term | Category |
|---------------|-------------|----------|
| notes | [domain term] | folder |
| inbox | [domain term] | folder |
| archive | [domain term] | folder |
| note (type) | [domain term] | note type |
| reduce | [domain term] | process phase |
| reflect | [domain term] | process phase |
| reweave | [domain term] | process phase |
| verify | [domain term] | process phase |
| MOC | [domain term] | navigation |
| description | [domain term] | schema field |
| topics | [domain term] | schema field |
| [additional terms] | [domain terms] | [category] |

## Platform
- Tier: [Claude Code / Minimal]
- Automation level: [full / convention / manual]
- Automation: [full (default) / convention / manual]

## Active Feature Blocks
[Checked = included, unchecked = excluded with reason]
- [x] wiki-links -- always included (kernel)
- [x] maintenance -- always included (always)
- [x] self-evolution -- always included (always)
- [x] session-rhythm -- always included (always)
- [x] templates -- always included (always)
- [x] ethical-guardrails -- always included (always)
[List all conditional blocks with inclusion/exclusion rationale]

## Coherence Validation Results
- Hard constraints checked: [count]. Violations: [none / details]
- Soft constraints checked: [count]. Auto-adjusted: [details]. User-confirmed: [details]
- Compensating mechanisms active: [list or none]

## Failure Mode Risks
[Top 3-4 HIGH-risk failure modes for this domain from vulnerability matrix]

## Generation Parameters
- Folder names: [domain-specific folder names]
- Skills to generate: [all 26 — vocabulary-transformed]
- Hooks to generate: [orient, capture, validate, commit]
- Templates to create: [list]
- Topology: [single-agent / skills / fresh-context / orchestrated]

This file serves three purposes:

1. Immediate: Source of truth for all subsequent generation steps (context resilience)
2. Operational: Enables /architect to reason about configuration drift
3. Evolution: Enables /reseed to re-derive with updated understanding

---

Step 2: Folder Structure

Re-read ops/derivation.md at the start of this step for folder names and vocabulary mapping.

Create the three-space layout with domain-named directories:

[workspace]/
+-- [domain:notes]/          <-- structured knowledge (flat)
+-- [domain:inbox]/          <-- zero-friction capture (if processing >= moderate)
+-- [domain:archive]/        <-- processed, inactive
+-- self/                    <-- agent's persistent mind
|   +-- identity.md          <-- (created in Step 4)
|   +-- methodology.md       <-- (created in Step 5)
|   +-- goals.md             <-- (created in Step 6)
|   +-- relationships.md     <-- (optional, if domain involves people)
|   +-- memory/              <-- atomic personal insights
+-- templates/               <-- note templates (created in Step 8)
+-- ops/                     <-- operational coordination (already exists from Step 1)
|   +-- observations/        <-- atomic friction signals (Primitive 12)
|   +-- tensions/            <-- contradiction tracking (Primitive 12)
|   +-- methodology/         <-- vault self-knowledge (Primitive 14)
|   +-- queue/               <-- unified task queue (pipeline + maintenance)
|   |   +-- archive/         <-- completed task batches
|   +-- sessions/            <-- session tracking

The ops/observations/ and ops/tensions/ directories are required by Kernel Primitive 12 (Operational Learning Loop). They accumulate friction signals that /{DOMAIN:rethink} reviews when observation or tension counts exceed thresholds.

The inbox folder is always generated. It provides zero-friction capture regardless of processing level.

---

Step 3: Context File

Re-read ops/derivation.md at the start of this step for vocabulary mapping, personality dimensions, active block list, platform tier, and generation parameters.

This is the most critical generation step. The context file IS the system.

For Claude Code: Generate CLAUDE.md using ${CLAUDE_PLUGIN_ROOT}/generators/claude-md.md template. For Minimal: Generate README.md as self-contained conventions document.

Context file composition algorithm:

Step 1: Read generator template for the platform.

Step 2: Select feature blocks from ${CLAUDE_PLUGIN_ROOT}/generators/features/.
  Always-included blocks (11): wiki-links, processing-pipeline, schema, maintenance, self-evolution, methodology-knowledge, session-rhythm, templates, ethical-guardrails, helper-functions, graph-analysis
  Conditional blocks: based on derived dimensions (see Active Feature Blocks in derivation.md)

Step 3: Process blocks SEQUENTIALLY. For each selected block:
  a. Read the block file
  b. Apply vocabulary transformation (Section 9 algorithm -- LLM-based contextual replacement, NOT string find-replace)
  c. Compose into the growing context file
  d. Release the block from context before reading the next

Step 4: Compose in canonical block order:
  1. Philosophy (derived from personality + domain)
  2. session-rhythm -- Orient, work, persist, session capture
  3. atomic-notes -- Note design principles (if active)
  4. wiki-links -- Link philosophy and patterns
  5. mocs -- Navigation structure (if active)
  6. processing-pipeline -- Processing approach (always included)
  7. semantic-search -- Discovery layers (if active)
  8. schema -- Metadata and query patterns (always included)
  9. maintenance -- Health checks and reweaving
  10. self-evolution -- System evolution approach
  10b. methodology-knowledge -- Querying and consulting self-knowledge
  11. personality -- Voice and identity (if active)
  12. templates -- Template usage
  13. multi-domain -- Cross-domain rules (if active)
  14. self-space -- Agent identity and memory (if active)
  15. ethical-guardrails -- Behavioral constraints
  16. helper-functions -- Utility scripts (always included)
  17. graph-analysis -- Graph intelligence and query patterns (always included)

Step 5: Cross-reference elimination.
  If a block is excluded, scan remaining blocks for references to excluded concepts and remove or rephrase:
  - semantic-search excluded -> rephrase "semantic search" to "search your notes" or remove
  - mocs excluded -> simplify "topic MOCs" to "topic organization"
  - self-space excluded -> references to self/identity.md route to ops/ equivalents
  - atomic-notes excluded -> simplify atomicity references to general note guidance
  - multi-domain excluded -> remove cross-domain references

Step 6: Add required sections that are NOT from feature blocks:
  a. Header with philosophy statement and domain identity
  b. Discovery-first design section (kernel primitive 11)
  c. Memory type routing table (where content goes: notes/, self/, ops/, inbox/, reminders.md)
  d. Infrastructure routing table (routes methodology questions to arscontexta plugin skills)
  e. Self-improvement loop (manual friction capture instructions)
  f. Common Pitfalls (3-4 HIGH-risk failure modes from vulnerability matrix, in domain vocabulary)
  g. System Evolution section (architect, reseed, friction-driven growth)
  h. Self-extension blueprints (how to build new skills, hooks)
  i. Derivation Rationale summary (which dimensions, which signals, which tradition)
  j. Pipeline Compliance (NEVER write directly to notes/, route through inbox)
  k. Condition-based maintenance documentation (what signals trigger which actions)

Step 7: Coherence verification.
  - [ ] No orphaned references to excluded blocks
  - [ ] Vocabulary consistent (same universal term -> same domain term everywhere)
  - [ ] Personality tone consistent across all sections
  - [ ] All mentioned skills exist in the generated skills (or are documented as dormant tiers)
  - [ ] All mentioned file paths exist in the generated folder structure
  - [ ] All mentioned templates exist in the generated templates
  - [ ] Processing terminology matches selected pipeline approach (light vs heavy)
  - [ ] Schema fields mentioned in prose exist in generated templates

Step 8: Apply vocabulary transformation one final time.
  Read the completed context file. Replace every remaining universal term with its domain-native equivalent.
  The vocabulary test: would a domain user ever see a term from a different discipline?

Step 9: Write the file.
  Target operational density: each section should have enough detail that the agent can follow instructions without asking questions.
  "Process your notes" is insufficient.
  "Read the source fully, extract insights that serve the domain, check for duplicates" is sufficient.

Structural Marker Protection: Vocabulary transformation must NEVER touch structural markers. Field names in YAML (description:, topics:, relevant_notes:, type:, status:, _schema:) are structural and stay universal. Domain vocabulary applies to VALUES, prose content, and user-facing labels -- never to YAML field names or structural syntax.

CRITICAL quality requirements for the generated context file:

• Tell the agent to ALWAYS read self/ at session start
• Explain prose-as-title with examples from the user's domain
• Include domain-specific schema in the YAML section
• Provide self-extension blueprints
• Include derivation rationale (which dimensions, which signals)
• Feel cohesive, not like assembled blocks
• Use domain-native vocabulary throughout

---

Step 4: self/identity.md

Re-read ops/derivation.md for personality dimensions, vocabulary mapping, and use case context.

Generate identity.md with personality expressed as natural self-description, not configuration syntax.

If personality is derived (personality.enabled = true), use the personality x artifact transformation matrix from the personality-layer reference. If neutral-helpful (default), write clear, direct, professional self-description.

---
description: Who I am and how I approach my work
type: moc
---

# identity

[Adapted to use case and personality. Examples:
- Research: "I am a research partner building understanding about..."
- Therapy (warm): "I pay attention to what you write about your sessions..."
- PM (neutral): "I track decisions across your projects..."
- Companion (warm): "I remember the things that matter about your life..."]

## Core Values
- [Relevant values for the use case, derived from personality + domain]

## Working Style
- [How the agent approaches its work, reflecting personality dimensions]

---

Topics:
- [[methodology]]

---

Step 5: self/methodology.md

Re-read ops/derivation.md for processing level, vocabulary mapping, and domain context.

---
description: How I process, connect, and maintain knowledge
type: moc
---

# methodology

## Principles
- Prose-as-title: every [domain:note] is a proposition
- Wiki links: connections as graph edges
- [domain:MOCs]: attention management hubs
- Capture fast, process slow

## My Process
[Adapted to use case using domain-native language for the processing phases.
Use the vocabulary from derivation.md -- "surface" not "reduce" for therapy, etc.]

---

Topics:
- [[identity]]

---

Step 5f: ops/methodology/ (Vault Self-Knowledge)

Re-read ops/derivation.md for all dimension choices, platform tier, automation level, active feature blocks, and coherence validation results. This step creates the vault's self-knowledge folder required by Kernel Primitive 14 (methodology-folder).

Create ops/methodology/methodology.md (MOC):

---
description: The vault's self-knowledge — derivation rationale, configuration state, and operational evolution history
type: moc
---
# methodology

This folder records what the system knows about its own operation — why it was configured this way, what the current state is, and how it has evolved. Meta-skills (/{DOMAIN:rethink}, /{DOMAIN:architect}) read from and write to this folder. /{DOMAIN:remember} captures operational corrections here.

## Derivation Rationale
- [[derivation-rationale]] — Why each configuration dimension was set the way it was

## Configuration State
(Populated by /{DOMAIN:rethink}, /{DOMAIN:architect})

## Evolution History
(Populated by /{DOMAIN:rethink}, /{DOMAIN:architect}, /{DOMAIN:reseed})

## How to Use This Folder

Browse notes: `ls ops/methodology/`
Query by category: `rg '^category:' ops/methodology/`
Find active directives: `rg '^status: active' ops/methodology/`
Ask the research graph: `/ask [question about your system]`

Meta-skills (/{DOMAIN:rethink}, /architect) read from and write to this folder.
/{DOMAIN:remember} captures operational corrections here.

Create ops/methodology/derivation-rationale.md (initial note):

---
description: Why each configuration dimension was chosen — the reasoning behind initial system setup
category: derivation-rationale
created: {timestamp}
status: active
---
# derivation rationale for {domain}

{Extract from ops/derivation.md the key dimension choices and the conversation signals that drove them. Include: platform tier, automation level, active feature blocks, and coherence validation results. Write in prose format, not raw transcript — synthesize the reasoning into a readable narrative that future meta-skills can consult.}

---

Topics:
- [[methodology]]

The seven content categories for ops/methodology/ are: derivation-rationale, kernel-state, pipeline-config, maintenance-conditions, vocabulary-map, configuration-state, drift-detection. Only derivation-rationale is created at init; the others are populated by meta-skills during operation.

---

Step 5g: manual/ (User-Navigable Documentation)

Re-read ops/derivation.md for vocabulary mapping and domain context.

Generate all 7 manual pages using domain-native vocabulary from the derivation conversation. The manual is self-contained user documentation — pages wiki-link to each other but NOT to notes/.

Generation instructions:

For each page, apply vocabulary transformation: replace universal terms (notes, inbox, topic map, reduce, reflect, reweave) with domain-native equivalents from the derivation conversation. Use concrete domain examples where possible.

Page 1: manual.md (Hub MOC)

---
description: User manual for your {domain} knowledge system
type: manual
generated_from: "arscontexta-{version}"
---
# Manual

Welcome to your {domain} knowledge system. This manual explains how everything works.

## Pages

- [[getting-started]] — Your first session, first {DOMAIN:note}, and first connection
- [[skills]] — Every available command with when to use it and examples
- [[workflows]] — The processing pipeline, maintenance cycle, and session rhythm
- [[configuration]] — How to adjust settings via config.yaml or /architect
- [[meta-skills]] — /ask, /architect, /{DOMAIN:rethink}, and /{DOMAIN:remember} explained
- [[troubleshooting]] — Common issues and how to resolve them

Page 2: getting-started.md

---
description: First session guide — creating your first {DOMAIN:note} and building connections
type: manual
generated_from: "arscontexta-{version}"
---
# Getting Started

{Generate content covering:}
- What to expect in your first session
- Creating your first {DOMAIN:note} (walk through the process)
- How connections work (wiki links, {DOMAIN:topic maps})
- The orient-work-persist session rhythm
- Where to go next (link to [[workflows]] and [[skills]])
- Running /tutorial for an interactive walkthrough

Page 3: skills.md

---
description: Complete reference for every available command
type: manual
generated_from: "arscontexta-{version}"
---
# Skills

{Generate content covering:}
- Every generated skill with domain-native name, purpose, and example invocation
- Group by category: Processing, Orchestration, Meta-Cognitive, Diagnostic, Knowledge, Research, Lifecycle, Onboarding
- For each skill: when to use it, what it does, example command
- Link to [[workflows]] for how skills chain together
- Link to [[meta-skills]] for detailed meta-skill documentation

Page 4: workflows.md

---
description: Processing pipeline, maintenance cycle, and session rhythm
type: manual
generated_from: "arscontexta-{version}"
---
# Workflows

{Generate content covering:}
- The full processing pipeline: {DOMAIN:seed} -> {DOMAIN:process} -> {DOMAIN:connect} -> {DOMAIN:maintain} -> {DOMAIN:verify}
- Session rhythm: orient (what's happening) -> work (do the thing) -> persist (save state)
- Maintenance cycle: condition-based triggers, what to do when conditions fire
- Batch processing with /{DOMAIN:orchestrate}
- Link to [[skills]] for command details
- Link to [[configuration]] for adjusting pipeline settings

Page 5: configuration.md

---
description: How to adjust your system via config.yaml and /architect
type: manual
generated_from: "arscontexta-{version}"
---
# Configuration

{Generate content covering:}
- config.yaml structure and key fields
- Using /architect for guided configuration changes
- Feature toggling: what can be enabled/disabled
- Preset explanation: what your preset includes and why
- Dimension positions and what they mean for your domain
- Link to [[meta-skills]] for /architect details
- Link to [[troubleshooting]] for configuration issues

Page 6: meta-skills.md

---
description: Deep guide to /ask, /architect, /{DOMAIN:rethink}, and /{DOMAIN:remember}
type: manual
generated_from: "arscontexta-{version}"
---
# Meta-Skills

{Generate content covering:}
- /ask — querying the bundled research knowledge base + local methodology
- /architect — getting research-backed configuration advice
- /{DOMAIN:rethink} — reviewing accumulated observations and tensions, drift detection
- /{DOMAIN:remember} — capturing friction and methodology learnings (Rule Zero: methodology as spec)
- When to use each meta-skill
- How meta-skills relate to system evolution
- Link to [[configuration]] for config changes
- Link to [[troubleshooting]] for drift-related issues

Page 7: troubleshooting.md

---
description: Common issues and resolution patterns
type: manual
generated_from: "arscontexta-{version}"
---
# Troubleshooting

{Generate content covering:}
- Orphan {DOMAIN:notes} — notes with no incoming links (run /{DOMAIN:connect})
- Dangling links — wiki links to non-existent {DOMAIN:notes} (check after renames)
- Stale content — {DOMAIN:notes} not updated in 30+ days with sparse connections (run /{DOMAIN:maintain})
- Methodology drift — system behavior diverging from methodology spec (run /{DOMAIN:rethink} drift)
- Inbox overflow — too many items accumulating (run /{DOMAIN:process} or /{DOMAIN:pipeline})
- Pipeline stalls — tasks stuck in queue (check with /{DOMAIN:next})
- Common mistakes table with corrections
- Link to [[meta-skills]] for /rethink and /remember
- Link to [[configuration]] for threshold adjustments

Quality gates:

• All skill references use domain-native names from the derivation conversation
• All pages link back to [[manual]] via a footer or contextual reference
• No wiki links to notes/ — manual is self-contained
• Each page has generated_from: "arscontexta-{version}" in frontmatter
• Content uses domain-specific examples, not generic/abstract ones

---

Step 6: self/goals.md

Re-read ops/derivation.md for use case context.

---
description: Current active threads and what I am working on
type: moc
---

# goals

## Active Threads
- Getting started -- learning this knowledge system
- [Use-case-specific initial goals derived from conversation]

## Completed
(none yet)

---

Topics:
- [[identity]]

---

Step 7: ops/config.yaml

Re-read ops/derivation.md for all dimension positions and feature states.

Generate the human-editable configuration file:

# ops/config.yaml -- edit these to adjust your system
# See ops/derivation.md for WHY each choice was made

dimensions:
  granularity: [atomic | moderate | coarse]
  organization: [flat | hierarchical]
  linking: [explicit | implicit | explicit+implicit]
  processing: [light | moderate | heavy]
  navigation: [2-tier | 3-tier]
  maintenance: condition-based
  schema: [minimal | moderate | dense]
  automation: [manual | convention | full]

features:
  semantic-search: [true | false]
  processing-pipeline: [true | false]
  sleep-processing: [true | false]
  voice-capture: false

processing_tier: auto    # auto | 1 | 2 | 3 | 4

processing:
  depth: standard          # deep | standard | quick
  chaining: suggested      # manual | suggested | automatic
  extraction:
    selectivity: moderate  # strict | moderate | permissive
    categories: auto       # auto (from derivation) | custom list
  verification:
    description_test: true
    schema_check: true
    link_check: true
  reweave:
    scope: related         # related | broad | full
    frequency: after_create # after_create | periodic | manual

provenance: [full | minimal | off]

personality:
  enabled: [true | false]

research:
  primary: [exa-deep-research | web-search]    # best available research tool
  fallback: [exa-web-search | web-search]      # fallback if primary unavailable
  last_resort: web-search                       # always available
  default_depth: moderate                       # light | moderate | deep

Processing depth levels:

• deep -- Full pipeline, fresh context per phase, maximum quality gates. Best for important sources and initial vault building.
• standard -- Full pipeline, balanced attention. Regular processing, moderate volume.
• quick -- Compressed pipeline, combine connect+verify phases. High volume catch-up, minor sources.

Pipeline chaining modes:

• manual -- Skills output "Next: /[skill] [target]" -- user decides.
• suggested -- Skills output next step AND add to task queue -- user can skip.
• automatic -- Skills complete → next phase runs immediately via orchestration.

Research tool detection: During generation, check for available research tools:

1. If Exa MCP tools available (mcp__exa__deep_researcher_start): primary = exa-deep-research
2. If Exa web search available (mcp__exa__web_search_exa): fallback = exa-web-search
3. Web search is always the last resort

Relationship: config.yaml is the live operational config. derivation.md is the historical record of WHY. Config can drift; /architect detects and documents the drift.

---

Step 7b: ops/derivation-manifest.md (Runtime Vocabulary for Inherited Skills)

Re-read ops/derivation.md for all dimension positions, vocabulary mapping, active blocks, and platform information.

Generate the machine-readable derivation manifest. This is the KEY file that enables runtime vocabulary transformation for all inherited processing skills (/reduce, /reflect, /reweave, /verify, /validate). Skills read this file at invocation time to apply domain-specific vocabulary without needing domain-specific skill copies.

# ops/derivation-manifest.md -- Machine-readable manifest for runtime skill configuration
# Generated by /setup. Updated by /reseed, /architect, /add-domain.
---
engine_version: "0.2.0"
research_snapshot: "2026-02-10"
generated_at: [ISO 8601 timestamp]
platform: [claude-code | minimal]
kernel_version: "1.0"

dimensions:
  granularity: [atomic | moderate | coarse]
  organization: [flat | hierarchical]
  linking: [explicit | implicit | explicit+implicit]
  processing: [light | moderate | heavy]
  navigation: [2-tier | 3-tier]
  maintenance: condition-based
  schema: [minimal | moderate | dense]
  automation: [manual | convention | full]

active_blocks:
  - [list of active feature block IDs]

coherence_result: [passed | passed_with_warnings]

vocabulary:
  # Level 1: Folder names
  notes: "[domain term]"        # e.g., "claims", "reflections", "decisions"
  inbox: "[domain term]"        # e.g., "inbox", "captures", "incoming"
  archive: "[domain term]"      # e.g., "archive", "processed", "completed"
  ops: "ops"                    # always ops

  # Level 2: Note types
  note: "[domain term]"         # e.g., "claim", "reflection", "decision"
  note_plural: "[domain term]"  # e.g., "claims", "reflections", "decisions"

  # Level 3: Schema field names
  description: "[domain term]"  # e.g., "description", "summary", "brief"
  topics: "[domain term]"       # e.g., "topics", "themes", "areas"
  relevant_notes: "[domain term]" # e.g., "relevant notes", "connections", "related"

  # Level 4: Navigation terms
  topic_map: "[domain term]"    # e.g., "topic map", "theme", "decision register"
  hub: "[domain term]"          # e.g., "hub", "home", "overview"

  # Level 5: Process verbs
  reduce: "[domain term]"       # e.g., "reduce", "surface", "document"
  reflect: "[domain term]"      # e.g., "reflect", "find patterns", "link decisions"
  reweave: "[domain term]"      # e.g., "reweave", "revisit", "update"
  verify: "[domain term]"       # e.g., "verify", "check resonance", "validate"
  validate: "[domain term]"     # e.g., "validate", "check schema", "audit"
  rethink: "[domain term]"      # e.g., "rethink", "reassess", "retrospect"

  # Level 6: Command names (as users invoke them)
  cmd_reduce: "[/domain-verb]"  # e.g., "/reduce", "/surface", "/document"
  cmd_reflect: "[/domain-verb]" # e.g., "/reflect", "/find-patterns", "/link-decisions"
  cmd_reweave: "[/domain-verb]" # e.g., "/reweave", "/revisit", "/update-old"
  cmd_verify: "[/domain-verb]"  # e.g., "/verify", "/check", "/audit"
  cmd_rethink: "[/domain-verb]" # e.g., "/rethink", "/reassess", "/retrospect"

  # Level 7: Extraction categories (domain-specific, from conversation)
  extraction_categories:
    - name: "[category name]"
      what_to_find: "[description]"
      output_type: "[note type]"
    - name: "[category name]"
      what_to_find: "[description]"
      output_type: "[note type]"
    # ... 4-8 domain-specific categories

platform_hints:
  context: [fork | single]
  allowed_tools: [tool list based on platform tier]
  semantic_search_tool: [mcp__qmd__deep_search | null]
  semantic_search_autoapprove:
    - mcp__qmd__search
    - mcp__qmd__vector_search
    - mcp__qmd__deep_search
    - mcp__qmd__get
    - mcp__qmd__multi_get
    - mcp__qmd__status

personality:
  warmth: [clinical | warm | playful]
  opinionatedness: [neutral | opinionated]
  formality: [formal | casual]
  emotional_awareness: [task-focused | attentive]
---

Why this file exists separately from derivation.md: derivation.md is the human-readable reasoning record (WHY each choice was made, conversation signals, confidence levels). derivation-manifest.md is the machine-readable operational manifest (WHAT the choices are). Skills read the manifest for quick vocabulary lookup without parsing the narrative derivation document.

Who updates this file:

• /setup generates it
• /reseed regenerates it after re-derivation
• /architect updates it when implementing approved changes
• /add-domain extends it with new domain vocabulary

---

Step 8: Templates with _schema blocks

Re-read ops/derivation.md for schema level, vocabulary mapping, and domain-specific field requirements.

Create domain-specific templates in templates/:

Always create:

• Primary note template (domain-named: claim-note.md, reflection-note.md, decision-note.md, etc.)
• MOC template (domain-named: topic-map.md, theme.md, decision-register.md, etc.)

Conditionally create:

• Source capture template (if processing >= moderate)
• Observation template (if self-evolution is active -- always)

Each template MUST include a _schema block defining required fields, optional fields, enums, and constraints. The template IS the single source of truth for schema.

Template structure:

---
_schema:
  entity_type: "[domain]-note"
  applies_to: "[domain:notes]/*.md"
  required:
    - description
    - topics
  optional:
    - [domain-specific fields based on schema density]
  enums:
    type:
      - [domain-relevant types]
  constraints:
    description:
      max_length: 200
      format: "One sentence adding context beyond the title"
    topics:
      format: "Array of wiki links"

# Template fields
description: ""
topics: []
[domain fields with defaults]
---

# {prose-as-title}

{Content}

---

Relevant Notes:
- [[related note]] -- relationship context

Topics:
- [[relevant-moc]]

Apply vocabulary transformation to the template: field labels in comments and example values use domain vocabulary. YAML field names stay structural (description, topics, etc.).

---

Step 9: Skills (vocabulary-transformed, full suite)

Re-read ops/derivation.md for processing level, platform, vocabulary mapping, and skills list.

Generate ALL skills for the detected platform. Every vault ships with the complete skill set from day one. Full automation is the default — users opt down, never up.

Skill source templates live at ${CLAUDE_PLUGIN_ROOT}/skill-sources/. Each subdirectory contains a SKILL.md template that must be read, vocabulary-transformed, and written to the user's skills directory.

The 16 skill sources to install:

Source Directory	Skill Name	Category
${CLAUDE_PLUGIN_ROOT}/skill-sources/reduce/	reduce	Processing
${CLAUDE_PLUGIN_ROOT}/skill-sources/reflect/	reflect	Processing
${CLAUDE_PLUGIN_ROOT}/skill-sources/reweave/	reweave	Processing
${CLAUDE_PLUGIN_ROOT}/skill-sources/verify/	verify	Processing
${CLAUDE_PLUGIN_ROOT}/skill-sources/validate/	validate	Processing
${CLAUDE_PLUGIN_ROOT}/skill-sources/seed/	seed	Orchestration
${CLAUDE_PLUGIN_ROOT}/skill-sources/ralph/	ralph	Orchestration
${CLAUDE_PLUGIN_ROOT}/skill-sources/pipeline/	pipeline	Orchestration
${CLAUDE_PLUGIN_ROOT}/skill-sources/tasks/	tasks	Orchestration
${CLAUDE_PLUGIN_ROOT}/skill-sources/stats/	stats	Navigation
${CLAUDE_PLUGIN_ROOT}/skill-sources/graph/	graph	Navigation
${CLAUDE_PLUGIN_ROOT}/skill-sources/next/	next	Navigation
${CLAUDE_PLUGIN_ROOT}/skill-sources/learn/	learn	Growth
${CLAUDE_PLUGIN_ROOT}/skill-sources/remember/	remember	Growth
${CLAUDE_PLUGIN_ROOT}/skill-sources/rethink/	rethink	Evolution
${CLAUDE_PLUGIN_ROOT}/skill-sources/refactor/	refactor	Evolution

For each skill:

1. Read ${CLAUDE_PLUGIN_ROOT}/skill-sources/[name]/SKILL.md
2. Apply vocabulary transformation — rename and update ALL internal references using the vocabulary mapping from ops/derivation.md
3. Adjust skill metadata (set context: fork for fresh context per invocation)
4. Write the transformed SKILL.md to the user's skills directory

For Claude Code: Write to .claude/skills/[domain-skill-name]/SKILL.md

CRITICAL: Do NOT generate skills from scratch or improvise their content. Read the source template and transform it. The templates contain quality gates, anti-shortcut language, and handoff formats that must be preserved.

Every generated skill must include:

• Anti-shortcut language for quality-critical steps
• Quality gates with explicit pass/fail criteria
• Handoff block format for orchestrated execution
• Domain-native vocabulary throughout

Skill Discoverability Protocol

Platform limitation: Claude Code's skill index does not refresh mid-session. Skills created during /setup are not discoverable until the user restarts Claude Code.

After creating ALL skill files:

1. Inform the user: Display "Generated [N] skills. Restart Claude Code to activate them."
2. Add to context file: Include a "Recently Created Skills (Pending Activation)" section listing all generated skills with their domain-native names and creation timestamp:

## Recently Created Skills (Pending Activation)

These skills were created during initialization. Restart Claude Code to activate them.
- /[domain:reduce] -- Extract insights from source material (created [timestamp])
- /[domain:reflect] -- Find connections between [domain:notes] (created [timestamp])
...

3. SessionStart hook detects activation: The session-orient.sh hook checks for this section. Once skills are confirmed loaded (appear in skill index), the section can be removed from the context file.
4. Phase 6 guidance: If any skills were created, Phase 6 output includes: "Restart Claude Code now to activate all skills, then try /[domain:help] to see what's available."

---

Step 10: Hooks (platform-appropriate)

Re-read ops/derivation.md for automation level, platform tier, and vocabulary mapping.

Additive Hook Merging Protocol

Generated hooks MUST NOT overwrite existing user hooks. Before writing any hooks:

1. Read existing .claude/settings.json (if it exists)
2. Parse existing hook matcher groups for each event type (hooks.SessionStart, hooks.PostToolUse, hooks.Stop, etc.)
3. ADD new matcher groups to the event arrays -- never replace existing entries
4. If a matcher group with the same command path already exists for that event, SKIP it (warn in output, don't overwrite)
5. Write the merged result back to .claude/settings.json

Validation criterion: After hook generation, all pre-existing hooks are still present and functional.

Session Persistence Architecture

Session persistence is critical for continuity across /clear and session restarts.

Session data layout:

ops/
├── sessions/
│   ├── current.json          # Active session state (updated by hooks)
│   └── YYYYMMDD-HHMMSS.json  # Archived session records
├── goals.md                  # Persistent working memory (survives /clear)
└── config.yaml               # Live configuration

current.json tracks: session_id, start_time, notes_created (array), notes_modified (array), discoveries (array), last_activity timestamp.

Session ID derivation: Use CLAUDE_CONVERSATION_ID environment variable (available in Claude Code hook environment). Fallback to timestamp: $(date +%Y%m%d-%H%M%S).

Session restore on /clear: When a user runs /clear, SessionStart fires for the new conversation. The hook detects existing session data (goals.md, ops/ state), re-reads everything, and provides continuity despite context reset.

Full Hook Suite (generated for all systems)

For Claude Code, add to .claude/settings.json (using additive merge).

Hook format: Claude Code uses a nested matcher-group structure. Each event type contains an array of matcher groups, each with an optional matcher (regex string filtering when the hook fires) and a hooks array of handler objects. Events like SessionStart and Stop don't need matchers — omit the field. Tool events like PostToolUse use the tool name as matcher (e.g., "Write", "Edit|Write"). Timeout is in seconds.

{
  "hooks": {
    "SessionStart": [
      {
        "hooks": [
          {
            "type": "command",
            "command": "bash .claude/hooks/session-orient.sh"
          }
        ]
      }
    ],
    "PostToolUse": [
      {
        "matcher": "Write",
        "hooks": [
          {
            "type": "command",
            "command": "bash .claude/hooks/validate-note.sh"
          },
          {
            "type": "command",
            "command": "bash .claude/hooks/auto-commit.sh",
            "async": true
          }
        ]
      }
    ],
    "Stop": [
      {
        "hooks": [
          {
            "type": "command",
            "command": "bash .claude/hooks/session-capture.sh"
          }
        ]
      }
    ]
  }
}

Critical: The old flat format ("type": "command" at the matcher level) is rejected by Claude Code. Each event must use the nested structure: "EventName": [{ "matcher": "...", "hooks": [{ "type": "command", "command": "..." }] }].

Generate all four hook scripts: session-orient.sh, session-capture.sh, validate-note.sh, auto-commit.sh.

---

Step 11: Hub MOC

Re-read ops/derivation.md for vocabulary mapping and use case context.

Create the vault entry point at [domain:notes]/index.md:

---
description: Entry point to the knowledge system -- start here to navigate
type: moc
---

# index

Welcome to your [domain] system.

## [domain:Topics]
[Links to self/ MOCs and any domain-specific topic MOCs that are relevant]
- [[identity]] -- who the agent is and how it approaches work
- [[methodology]] -- how the agent processes and connects knowledge
- [[goals]] -- current active threads

## Getting Started
1. Read self/identity.md to understand your purpose
2. Capture your first [domain:note] in [domain:notes]/
3. Connect it to this hub

---

Step 12: Semantic Search Setup (conditional)

Only if semantic-search feature is active (linking includes implicit).

1. Check if qmd is installed: which qmd
2. If installed:
   • Run qmd init in the generated vault root
   • Configure or update the qmd collection for {vocabulary.notes_collection} so it points at the generated notes directory
   • Create or merge .mcp.json in the vault root with this qmd MCP server contract:
     • {"mcpServers":{"qmd":{"command":"qmd","args":["mcp"],"autoapprove":["mcp__qmd__search","mcp__qmd__vector_search","mcp__qmd__deep_search","mcp__qmd__get","mcp__qmd__multi_get","mcp__qmd__status"]}}}
   • Run qmd update && qmd embed to build the initial index
3. If NOT installed:
   • Add a "Next Steps" section to the Phase 6 summary telling the user to install qmd
   • Include specific commands:
     • npm install -g @tobilu/qmd (or bun install -g @tobilu/qmd)
     • qmd init
     • qmd collection add . --name {vocabulary.notes_collection} --mask "**/*.md"
     • qmd update && qmd embed
   • Include the .mcp.json qmd MCP contract with autoapprove entries in setup output so activation is deterministic once qmd is installed

---

Step 13: Graph Query Scripts (derived from template schemas)

Re-read ops/derivation.md and the generated templates for schema fields.

After creating templates (Step 8), read the _schema blocks and generate domain-adapted analysis scripts in ops/queries/ (or scripts/queries/ for Claude Code).

Generation algorithm:

1. Read all _schema.required and _schema.optional fields from generated templates
2. Identify queryable dimensions (fields with enum values, date fields, array fields with wiki links)
3. For each meaningful 2-field combination, generate a ripgrep-based query script:
   • Cross-reference queries -- notes sharing one field value but differing on another
   • Temporal queries -- items older than N days in a given status
   • Density queries -- fields with few entries (gap detection)
   • Backlink queries -- what references a specific entity
4. Name each script descriptively

Generate 3-5 scripts appropriate for the domain. Examples:

Domain	Generated Queries
Therapy	trigger-mood-correlation.sh, recurring-triggers.sh, stale-patterns.sh
Research	cross-methodology.sh, low-confidence-candidates.sh, source-diversity.sh
Relationships	neglected-contacts.sh, topic-overlap.sh
PM	overdue-items.sh, owner-workload.sh, priority-distribution.sh

Include a discovery section in the context file documenting what queries exist, when to run them, and what insights they surface.

---

Step 14: ops/reminders.md

Always generated. Create an empty reminders file with format header:

# Reminders

<!-- Checked at session start. Due items surface in orientation. -->
<!-- Format: - [ ] YYYY-MM-DD: Description -->
<!-- Completed: - [x] YYYY-MM-DD: Description (done YYYY-MM-DD) -->

---

Step 15: Vault Marker

Create .arscontexta in the vault root. This marker file identifies the directory as an Ars Contexta vault (hooks only run when it exists) and doubles as the hook configuration file.

# Ars Contexta vault marker + config
# This file identifies the directory as an Ars Contexta vault.
# Do not delete — hooks only run when this file exists.

git: true
session_capture: true

Keys and defaults:

• git: true — auto-commit on writes (auto-commit.sh)
• session_capture: true — session JSON capture on start (session-orient.sh)

Omitted keys default to true, so a minimal marker file (or even an empty file) preserves full default behaviour.

---

Step 16: Git Initialization

git init
git add -A
git commit -m "Initial vault generation by Ars Contexta"

If git is already initialized (existing repo), skip git init and just commit the generated files.

---

PHASE 6: Validation and Summary

Kernel Validation

Run all 15 primitive checks against the generated system. Use ${CLAUDE_PLUGIN_ROOT}/reference/validate-kernel.sh if available. Otherwise manually verify:

1. markdown-yaml -- Every .md file has valid YAML frontmatter? (>95% threshold)
2. wiki-links -- All wiki links resolve to existing files? (>90% threshold)
3. moc-hierarchy -- At least 3 MOCs exist, every note appears in at least one MOC?
4. tree-injection -- Session start procedure loads file structure? (hook or context file instruction)
5. description-field -- Every note has a description field that differs from the title? (>95%)
6. topics-footer -- Topics field present on every non-MOC note? (>95%)
7. schema-enforcement -- Templates exist as single source of truth, validation mechanism present?
8. semantic-search -- Configured or documented for future activation?
9. self-space -- self/ exists with identity.md, methodology.md, goals.md?
10. session-rhythm -- Context file documents orient/work/persist cycle?
11. discovery-first -- Context file contains Discovery-First Design section, notes optimized for findability?
12. operational-learning-loop -- ops/observations/ and ops/tensions/ exist, review trigger documented in context file, /{DOMAIN:rethink} command exists?
13. task-stack -- ops/tasks.md exists? Queue file (ops/queue/queue.json) exists with schema_version >= 3 and maintenance_conditions section? Context file references both in session-orient phase? /{DOMAIN:next} command exists with condition reconciliation?
14. methodology-folder -- ops/methodology/ exists with methodology.md MOC? At least one derivation-rationale note exists? Context file references ops/methodology/ for meta-skill context?
15. session-capture -- ops/sessions/ directory exists? Session-end hook template installed? Condition-based mining trigger exists for unprocessed sessions?

Report results: pass/fail per primitive with specific failures listed.

Pipeline Smoke Test

After kernel validation, run a functional test:

1. Create a test note in [domain:notes]/ with a sample title and description
2. Verify it has correct schema (description, topics)
3. Verify the hub MOC can reference it
4. Delete the test note and clean up

If the smoke test fails, report the failure with specific remediation steps. A vault that passes structural validation but fails functional testing is not ready.

Clean CLI Output

Present results using clean formatting per Section 10.5 design language. No runes, no sigils, no decorative Unicode, no ASCII art. Clean indented text with standard markdown formatting only.

ars contexta -- the art of context

  Creating your [domain] structure...
  Writing your context file...
  Installing [domain:skills]...
  Setting up templates...
  Building your first [domain:topic map]...
  Initializing version control...
  Running validation...

Your memory is ready.

• Progress markers: Use indented text for generation milestones. These provide orientation during generation.
• Section dividers: Use --- (standard markdown) between major output sections.

Progressive Feature Reveal

Show available commands in the user's vocabulary. Resolve command names from ops/derivation-manifest.md vocabulary:

Here's what you can do:

  /arscontexta:[domain:reduce]    -- extract insights from source material
  /arscontexta:[domain:reflect]   -- find connections between your [domain:notes]
  /arscontexta:health             -- check your knowledge system
  /arscontexta:help               -- see everything available
  /arscontexta:next               -- get intelligent next-action recommendations
  /arscontexta:learn              -- research a topic and grow your graph

Note: Plugin commands use the format /arscontexta:command-name. List all commands explicitly since they may not appear in tab completion. If skills were generated, note they require a Claude Code restart.

First-Success Moment

Guide the user to capture their first note. This is where the system stops being abstract and becomes real.

If a preset was selected: Check ${CLAUDE_PLUGIN_ROOT}/presets/[preset]/starter/ for domain-specific starter notes. Use the most relevant starter as a seed:

1. Present a starter note appropriate to the domain (e.g., a research claim, a personal reflection, a project decision)
2. Ask the user: "Here's a starter [domain:note] to get you going. Want to customize it, or shall I save it as-is?"
3. Create the note in [domain:notes]/ with proper schema
4. Add it to the hub MOC
5. Show: the note, the MOC it landed in, the schema fields filled

If no preset: Guide open-ended: "Try capturing something: just tell me an idea." Then create the note and show the same result.

Why this matters: The first-success moment proves the system works. The user sees their content structured, connected, and navigable. This converts abstract architecture into tangible value.

Summary

Present in the user's vocabulary with clean formatting:

ars contexta

Your [domain] system is ready.

Configuration:
  Platform:        [Claude Code / Minimal]
  Automation: Full — all capabilities from day one
  [Key dimension highlights relevant to the user]

Created:
  [list of folders with domain names]
  [context file name]
  [templates created]
  16 skills generated (vocabulary-transformed)
  10 plugin commands available via /arscontexta:*
  [hooks configured]
  ops/derivation.md      -- the complete record of how this system was derived
  ops/derivation-manifest.md -- machine-readable config for runtime skills
  ops/methodology/       -- vault self-knowledge (query with /ask or browse directly)
  ops/config.yaml        -- edit this to adjust dimensions without re-running init

Kernel Validation: [PASS count] / 15 passed
[Any warnings to address]

IMPORTANT: Restart Claude Code now to activate skills and hooks.
  Skills and hooks take effect after restart — they are not available in the current session.

Next steps:
  1. Quit and restart Claude Code (required — skills won't work until you do)
  2. Read your CLAUDE.md -- it's your complete methodology
  3. Try /arscontexta:help to see all available commands
  4. [If qmd not installed: "Install qmd for semantic search: npm install -g @tobilu/qmd (or bun install -g @tobilu/qmd), then run qmd init, qmd update, qmd embed"]
  5. [If personality not enabled: "Run /arscontexta:architect later to tune the agent's voice"]
  6. Try /arscontexta:tutorial for a guided walkthrough

Conditional Next Steps

Include these based on system state:

• If qmd not installed and semantic-search is active: npm/bun install instructions + qmd init/update/embed + .mcp.json contract
• If personality not enabled: mention /arscontexta:architect for future voice tuning once the vault has 50+ notes
• If any kernel checks failed: specific remediation instructions

---

Quality Standards (Non-Negotiable)

These apply to every generation run. Do not shortcut any of them.

1. Generated files feel cohesive, not assembled from blocks. Block boundaries must be invisible in the output. The context file reads as if written from scratch for this specific domain.

2. Language matches the user's domain. A therapy user never sees "claim" or "reduce." A PM user never sees "reflection" or "surface." The vocabulary test applies to every generated file.

3. self/identity.md feels genuine, not templated. It reads like self-knowledge, not a character sheet.

4. Every generated file is immediately useful. No placeholder content. No "TODO: fill this in." Every file serves a purpose from day one.

5. Dimension settings are justified. The derivation rationale connects every choice to either a user signal or a research-backed default.

6. Kernel validation PASSES. Zero failures on every generated system. If validation fails, fix the generation before presenting results.

7. Vocabulary consistency across ALL files. The same universal term must ALWAYS map to the same domain term across all generated files. Run a mental consistency check: if you said "reflection" in the context file, you must say "reflection" in templates, skills, and self/ files.

8. Three-space boundaries are clean. Agent self-knowledge in self/. Domain knowledge in notes/. Operational scaffolding in ops/. No conflation.

9. Discovery-first is enforced. Every note, every MOC, every template is optimized for future agent discovery. Description quality, MOC membership, title composability.

10. Personality never contradicts methodology. A playful agent still enforces quality gates. A warm agent still requires composability checks. Personality affects HOW methodology is communicated, never WHETHER it is enforced.

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