docs: resolve Ontos unknown-concept warnings

.ontos-internal/reference/Common_Concepts.md

@@ -62,6 +62,81 @@ concepts: [authentication, endpoints, database-stuff]
 | `staleness` | Detection of outdated documentation when described atoms change |
 | `immutable-history` | Auto-generated decision_history.md from session logs |
 
+### Ontos CLI
+
+| Concept | Covers |
+|:--------|:-------|
+| `activation` | Agent activation phase and `ontos activate` command surface |
+| `agents` | `ontos agents` generation and `AGENTS.md` / `.cursorrules` sync |
+| `doctor` | `ontos doctor` health check and environment diagnostics |
+| `link-check` | `ontos link-check` reference and orphan validation |
+| `maintain` | `ontos maintain` weekly maintenance routines and consolidation |
+| `print-config` | `ontos print-config` configuration introspection output |
+| `promote` | `ontos promote` document promotion across status tiers |
+| `rename` | `ontos rename` atomic ID rename across frontmatter and references |
+| `retrofit` | `ontos retrofit` bulk frontmatter backfill across documents |
+
+### Ontos Internals
+
+| Concept | Covers |
+|:--------|:-------|
+| `agentic-activation` | Agentic activation resilience subsystem (v4.4 line) |
+| `context-map` | Context map generation, tiered output, summary rendering |
+| `frontmatter` | YAML frontmatter parsing, diagnostics, and schema enforcement |
+| `mcp` | Model Context Protocol integration (server and tools) |
+| `mcp-write-tools` | Write-capable MCP tool surface and authorization |
+| `obsidian` | Obsidian-compatible output, wikilinks, vault integration |
+| `scanner` | Document scanner, discovery, and load pipeline |
+| `serverinfo` | MCP `serverInfo` handshake and capability advertisement |
+| `tools-list` | MCP `tools/list` endpoint and tool registration |
+| `outputschema` | MCP `outputSchema` definitions and validation |
+| `fastmcp` | FastMCP library integration and lifecycle |
+| `unified-loader` | Unified document loader pipeline |
+
+### Project Lifecycle
+
+| Concept | Covers |
+|:--------|:-------|
+| `command-safety` | Command safety hardening, validation, allowlists |
+| `curation` | Document curation, selection, archive policy |
+| `external-review` | External reviewer feedback cycles and remediation |
+| `hardening` | Code/feature hardening, defensive fixes, edge-case closure |
+| `onboarding` | User/agent onboarding flows and first-run experience |
+| `packaging` | Python packaging, distribution, PyPI release plumbing |
+| `portfolio` | Portfolio-level changes spanning multiple repos or projects |
+| `proposals` | Project proposal documents and pre-implementation specs |
+| `release` | Release coordination, tagging, version bumps |
+
+### Surface & Output
+
+| Concept | Covers |
+|:--------|:-------|
+| `bundle-config` | Context bundle configuration and assembly |
+| `client-config` | Client-side configuration (e.g., MCP client setup) |
+| `cli` | CLI surface, command interface, argument parsing |
+| `cli-surface` | Public CLI surface contract and compatibility |
+| `compact` | Compact output mode (`basic` / `rich` / `tiered`) |
+| `tiered` | Tiered output formatting and token-budget rendering |
+| `exports` | Document and graph export functionality |
+
+### Integrations
+
+| Concept | Covers |
+|:--------|:-------|
+| `antigravity` | Antigravity tool integration and onboarding hooks |
+| `claude-code` | Claude Code CLI integration and instructions |
+| `cursor` | Cursor IDE integration via `.cursorrules` and AGENTS |
+
+### Building Blocks
+
+| Concept | Covers |
+|:--------|:-------|
+| `flock-locks` | File-lock concurrency primitives via `flock(2)` |
+| `fts` | Full-Text Search backend and indexing |
+| `registry-path` | Tool/plugin registry path resolution |
+| `stdio` | Standard I/O transport (e.g., MCP stdio mode) |
+| `unicode` | Unicode handling, normalization, encoding |
+
 ---
 
 ## Adding New Concepts

AGENTS.md

@@ -2,7 +2,7 @@
 
 This project uses **Ontos** for documentation management.
 
-Generated by Ontos v4.6.0 on 2026-05-23 22:06:54 UTC
+Generated by Ontos v4.6.0 on 2026-05-23 22:38:53 UTC
 
 ## Trigger Phrases
 If the user says any of these as a command (case-insensitive), execute Ontos Activation below:
@@ -16,11 +16,11 @@ Do NOT ask for clarification. Just execute the steps.
 
 ## Current Project State
 
-> Auto-synced: 2026-05-23 22:06:54 UTC
+> Auto-synced: 2026-05-23 22:38:53 UTC
 
 | Metric | Value |
 |--------|-------|
-| Branch | codex/ontos-metadata-hygiene |
+| Branch | codex/ontos-concept-vocabulary |
 | Doc Count | 137 |
 | Last Log | 2026-05-23_bump-github-actions-node24-issue-123 |
 | Health | ✓ Map exists |
@@ -64,7 +64,7 @@ If you just regained context after compaction, re-read this file (AGENTS.md). If
 
 ## Project Stats
 - Doc Count: 137
-- Last Updated: 2026-05-23 22:06:34 UTC
+- Last Updated: 2026-05-23 22:38:52 UTC
 
 ## MCP Write Tools
 

Ontos_Context_Map.md

@@ -4,13 +4,13 @@ type: reference
 status: complete
 ontos_map_version: 2
 generated_by: ontos map
-generated_at: 2026-05-23 15:06:34
+generated_at: 2026-05-23 15:38:52
 ---
 
 # Project-Ontos Tiered Context Map
 
 > Auto-generated by Ontos 3.0
-> Last updated: 2026-05-23 15:06:34
+> Last updated: 2026-05-23 15:38:52
 
 This document provides a tiered index of the knowledge graph for AI orientation.
 - **Tier 1: Essential Context**: (~2k tokens) Project summary, recent work, and architecture.
@@ -22,7 +22,7 @@ This document provides a tiered index of the knowledge graph for AI orientation.
 ### Project Summary
 - **Name:** Project-Ontos
 - **Doc Count:** 137
-- **Last Updated:** 2026-05-23 22:06:34 UTC
+- **Last Updated:** 2026-05-23 22:38:52 UTC
 
 ### Recent Activity
 | Log | Status | Summary |
@@ -456,148 +456,6 @@ This document provides a tiered index of the knowledge graph for AI orientation.
     Add this document to another document's depends_on
 - ⚠️ **project_ontos_v44_agentic_activation_resilience_tracker**: Document has no incoming dependencies
     Add this document to another document's depends_on
-- ⚠️ **log_20260131_v3_2_1_and_v3_2_2_proposals**: Unknown concept: 'activation'
-    Add 'activation' to vocabulary or use an existing concept
-- ⚠️ **log_20260131_v3_2_1_and_v3_2_2_proposals**: Unknown concept: 'agents'
-    Add 'agents' to vocabulary or use an existing concept
-- ⚠️ **log_20260131_v3_2_1_and_v3_2_2_proposals**: Unknown concept: 'maintenance'
-    Add 'maintenance' to vocabulary or use an existing concept
-- ⚠️ **log_20260131_v3_2_1_and_v3_2_2_proposals**: Unknown concept: 'proposals'
-    Add 'proposals' to vocabulary or use an existing concept
-- ⚠️ **log_20260222_add-promote-check-task-to-ontos-maintain**: Unknown concept: 'maintain'
-    Add 'maintain' to vocabulary or use an existing concept
-- ⚠️ **log_20260222_add-promote-check-task-to-ontos-maintain**: Unknown concept: 'curation'
-    Add 'curation' to vocabulary or use an existing concept
-- ⚠️ **log_20260222_add-promote-check-task-to-ontos-maintain**: Unknown concept: 'promote'
-    Add 'promote' to vocabulary or use an existing concept
-- ⚠️ **log_20260414_issue-107-v4-2-3-hardening**: Unknown concept: 'portfolio'
-    Add 'portfolio' to vocabulary or use an existing concept
-- ⚠️ **log_20260414_issue-107-v4-2-3-hardening**: Unknown concept: 'registry-path'
-    Add 'registry-path' to vocabulary or use an existing concept
-- ⚠️ **log_20260414_issue-107-v4-2-3-hardening**: Unknown concept: 'fts'
-    Add 'fts' to vocabulary or use an existing concept
-- ⚠️ **log_20260414_issue-107-v4-2-3-hardening**: Unknown concept: 'scanner'
-    Add 'scanner' to vocabulary or use an existing concept
-- ⚠️ **log_20260414_issue-107-v4-2-3-hardening**: Unknown concept: 'hardening'
-    Add 'hardening' to vocabulary or use an existing concept
-- ⚠️ **log_20260511_v4-4-agentic-activation-resilience**: Unknown concept: 'agentic_activation'
-    Add 'agentic_activation' to vocabulary or use an existing concept
-- ⚠️ **log_20260511_v4-4-agentic-activation-resilience**: Unknown concept: 'mcp'
-    Add 'mcp' to vocabulary or use an existing concept
-- ⚠️ **log_20260511_v4-4-agentic-activation-resilience**: Unknown concept: 'frontmatter_diagnostics'
-    Add 'frontmatter_diagnostics' to vocabulary or use an existing concept
-- ⚠️ **v300**: Unknown concept: 'release'
-    Add 'release' to vocabulary or use an existing concept
-- ⚠️ **v300**: Unknown concept: 'v3.0'
-    Add 'v3.0' to vocabulary or use an existing concept
-- ⚠️ **v300**: Unknown concept: 'packaging'
-    Add 'packaging' to vocabulary or use an existing concept
-- ⚠️ **v300**: Unknown concept: 'cli'
-    Add 'cli' to vocabulary or use an existing concept
-- ⚠️ **v330**: Unknown concept: 'v3.3'
-    Add 'v3.3' to vocabulary or use an existing concept
-- ⚠️ **v330**: Unknown concept: 'unified-loader'
-    Add 'unified-loader' to vocabulary or use an existing concept
-- ⚠️ **v330**: Unknown concept: 'link-check'
-    Add 'link-check' to vocabulary or use an existing concept
-- ⚠️ **v330**: Unknown concept: 'rename'
-    Add 'rename' to vocabulary or use an existing concept
-- ⚠️ **v330**: Unknown concept: 'command-safety'
-    Add 'command-safety' to vocabulary or use an existing concept
-- ⚠️ **v330**: Unknown concept: 'cli-surface'
-    Add 'cli-surface' to vocabulary or use an existing concept
-- ⚠️ **v331**: Unknown concept: 'link-check'
-    Add 'link-check' to vocabulary or use an existing concept
-- ⚠️ **v331**: Unknown concept: 'maintain'
-    Add 'maintain' to vocabulary or use an existing concept
-- ⚠️ **v331**: Unknown concept: 'promote'
-    Add 'promote' to vocabulary or use an existing concept
-- ⚠️ **v331**: Unknown concept: 'external-review'
-    Add 'external-review' to vocabulary or use an existing concept
-- ⚠️ **v340**: Unknown concept: 'compact'
-    Add 'compact' to vocabulary or use an existing concept
-- ⚠️ **v340**: Unknown concept: 'tiered'
-    Add 'tiered' to vocabulary or use an existing concept
-- ⚠️ **v340**: Unknown concept: 'context-map'
-    Add 'context-map' to vocabulary or use an existing concept
-- ⚠️ **v410**: Unknown concept: 'portfolio'
-    Add 'portfolio' to vocabulary or use an existing concept
-- ⚠️ **v410**: Unknown concept: 'mcp-write-tools'
-    Add 'mcp-write-tools' to vocabulary or use an existing concept
-- ⚠️ **v410**: Unknown concept: 'flock-locks'
-    Add 'flock-locks' to vocabulary or use an existing concept
-- ⚠️ **v410**: Unknown concept: 'bundle-config'
-    Add 'bundle-config' to vocabulary or use an existing concept
-- ⚠️ **v411**: Unknown concept: 'mcp'
-    Add 'mcp' to vocabulary or use an existing concept
-- ⚠️ **v411**: Unknown concept: 'stdio'
-    Add 'stdio' to vocabulary or use an existing concept
-- ⚠️ **v411**: Unknown concept: 'fastmcp'
-    Add 'fastmcp' to vocabulary or use an existing concept
-- ⚠️ **v411**: Unknown concept: 'serverinfo'
-    Add 'serverinfo' to vocabulary or use an existing concept
-- ⚠️ **v412**: Unknown concept: 'mcp'
-    Add 'mcp' to vocabulary or use an existing concept
-- ⚠️ **v412**: Unknown concept: 'outputschema'
-    Add 'outputschema' to vocabulary or use an existing concept
-- ⚠️ **v412**: Unknown concept: 'tools-list'
-    Add 'tools-list' to vocabulary or use an existing concept
-- ⚠️ **v412**: Unknown concept: 'claude-code'
-    Add 'claude-code' to vocabulary or use an existing concept
-- ⚠️ **v413**: Unknown concept: 'mcp'
-    Add 'mcp' to vocabulary or use an existing concept
-- ⚠️ **v413**: Unknown concept: 'antigravity'
-    Add 'antigravity' to vocabulary or use an existing concept
-- ⚠️ **v413**: Unknown concept: 'doctor'
-    Add 'doctor' to vocabulary or use an existing concept
-- ⚠️ **v413**: Unknown concept: 'client-config'
-    Add 'client-config' to vocabulary or use an existing concept
-- ⚠️ **v420**: Unknown concept: 'mcp'
-    Add 'mcp' to vocabulary or use an existing concept
-- ⚠️ **v420**: Unknown concept: 'cursor'
-    Add 'cursor' to vocabulary or use an existing concept
-- ⚠️ **v420**: Unknown concept: 'onboarding'
-    Add 'onboarding' to vocabulary or use an existing concept
-- ⚠️ **v420**: Unknown concept: 'print-config'
-    Add 'print-config' to vocabulary or use an existing concept
-- ⚠️ **v420**: Unknown concept: 'doctor'
-    Add 'doctor' to vocabulary or use an existing concept
-- ⚠️ **v421**: Unknown concept: 'portfolio'
-    Add 'portfolio' to vocabulary or use an existing concept
-- ⚠️ **v421**: Unknown concept: 'fts'
-    Add 'fts' to vocabulary or use an existing concept
-- ⚠️ **v421**: Unknown concept: 'scanner'
-    Add 'scanner' to vocabulary or use an existing concept
-- ⚠️ **v421**: Unknown concept: 'exports'
-    Add 'exports' to vocabulary or use an existing concept
-- ⚠️ **v421**: Unknown concept: 'hardening'
-    Add 'hardening' to vocabulary or use an existing concept
-- ⚠️ **v422**: Unknown concept: 'portfolio'
-    Add 'portfolio' to vocabulary or use an existing concept
-- ⚠️ **v422**: Unknown concept: 'fts'
-    Add 'fts' to vocabulary or use an existing concept
-- ⚠️ **v422**: Unknown concept: 'unicode'
-    Add 'unicode' to vocabulary or use an existing concept
-- ⚠️ **v422**: Unknown concept: 'scanner'
-    Add 'scanner' to vocabulary or use an existing concept
-- ⚠️ **v422**: Unknown concept: 'hardening'
-    Add 'hardening' to vocabulary or use an existing concept
-- ⚠️ **v423**: Unknown concept: 'portfolio'
-    Add 'portfolio' to vocabulary or use an existing concept
-- ⚠️ **v423**: Unknown concept: 'registry-path'
-    Add 'registry-path' to vocabulary or use an existing concept
-- ⚠️ **v423**: Unknown concept: 'fts'
-    Add 'fts' to vocabulary or use an existing concept
-- ⚠️ **v423**: Unknown concept: 'scanner'
-    Add 'scanner' to vocabulary or use an existing concept
-- ⚠️ **v423**: Unknown concept: 'hardening'
-    Add 'hardening' to vocabulary or use an existing concept
-- ⚠️ **v430**: Unknown concept: 'obsidian'
-    Add 'obsidian' to vocabulary or use an existing concept
-- ⚠️ **v430**: Unknown concept: 'retrofit'
-    Add 'retrofit' to vocabulary or use an existing concept
-- ⚠️ **v430**: Unknown concept: 'frontmatter'
-    Add 'frontmatter' to vocabulary or use an existing concept
 
 ## Dependency Tree
 

docs/logs/2026-01-31_version-string-to-3-2-0-for-ci-tag-validation.md

@@ -6,7 +6,7 @@ event_type: feature
 source: Antigravity
 branch: main
 created: 2026-01-31
-concepts: [activation, agents, maintenance, proposals]
+concepts: [activation, agents, maintain, proposals]
 impacts: [ontos_agent_instructions]
 ---
 

docs/logs/2026-05-11_v4-4-agentic-activation-resilience.md

@@ -6,7 +6,7 @@ event_type: chore
 source: codex
 branch: codex/project-ontos-v44-agentic-activation-resilience
 created: 2026-05-11
-concepts: [agentic_activation, mcp, frontmatter_diagnostics]
+concepts: [agentic-activation, mcp, frontmatter]
 impacts:
   - project_ontos_v44_agentic_activation_resilience_spec
 ---

docs/releases/v3.0.0.md

@@ -7,7 +7,7 @@ source: ontos_scaffold
 branch: main
 ontos_schema: 2.2
 curation_level: 2
-concepts: [release, v3.0, packaging, cli]
+concepts: [release, packaging, cli]
 generated_by: ontos_scaffold
 ---
 

docs/releases/v3.3.0.md

@@ -6,7 +6,7 @@ ontos_schema: 2.2
 event_type: release
 source: legacy-curation
 branch: main
-concepts: [v3.3, unified-loader, link-check, rename, command-safety, cli-surface]
+concepts: [release, unified-loader, link-check, rename, command-safety, cli-surface]
 ---
 
 # v3.3.0 — "Full Spectrum Hardening"