feat(#10): knowledge file format schema + example knowledge files

- SCHEMA.md: full specification for index.json and YAML knowledge files
- knowledge/global/pitfalls.yaml: 8 cross-repo pitfalls
- knowledge/global/tool-quirks.yaml: 7 environment quirk facts
- knowledge/repos/hermes-agent.yaml: 8 per-repo pitfalls (cron, paths, SSH)
- knowledge/repos/the-nexus.yaml: 6 per-repo pitfalls (merge, server, deploy)
- scripts/validate_knowledge.py: schema validator (29 facts, all passing)
- knowledge/index.json: populated with 29 seed facts from real fleet data

Design decisions:
- YAML for humans, index.json for machines
- ID format: domain:category:sequence for dedup and linking
- 5 categories: fact, pitfall, pattern, tool-quirk, question
- Confidence 0.0-1.0 with defined ranges
- Related facts by ID for graph traversal
- Tags for searchability
- Source count + dates for decay/expiry

Acceptance criteria:
- [x] Directory structure created
- [x] Schema documented (SCHEMA.md)
- [x] index.json with real facts (29 total)
- [x] Example knowledge files for 2 repos (hermes-agent, the-nexus)
- [x] Validation script passes

knowledge/SCHEMA.md

@@ -0,0 +1,114 @@
+# Knowledge File Format Specification
+
+**Version:** 1
+**Issue:** #10
+**Status:** Draft
+
+---
+
+## Overview
+
+The knowledge system has two layers:
+
+1. **index.json** — Machine-readable fact index. Fast lookups by ID, category, repo, tags.
+2. **Knowledge files** (YAML) — Human-readable, editable facts organized by domain.
+
+The harvester writes to both. The bootstrapper reads from index.json. Humans edit the YAML files directly.
+
+---
+
+## index.json Schema
+
+```json
+{
+  "version": 1,
+  "last_updated": "ISO-8601 timestamp",
+  "total_facts": 0,
+  "facts": []
+}
+```
+
+### Fact Object
+
+| Field | Type | Required | Description |
+|-------|------|----------|-------------|
+| `id` | string | yes | Unique identifier: `{domain}:{category}:{sequence}` |
+| `fact` | string | yes | One-sentence description of the knowledge |
+| `category` | enum | yes | One of: `fact`, `pitfall`, `pattern`, `tool-quirk`, `question` |
+| `domain` | string | yes | Where this applies: repo name, `global`, or agent name |
+| `confidence` | float | yes | 0.0–1.0. How certain is this knowledge? |
+| `tags` | string[] | no | Searchable labels |
+| `source_count` | int | no | How many sessions confirmed this fact |
+| `first_seen` | date | no | ISO-8601 date first extracted |
+| `last_confirmed` | date | no | ISO-8601 date last seen in a session |
+| `expires` | date | no | Optional. After this date, fact is stale |
+| `related` | string[] | no | IDs of related facts |
+
+### ID Format: `{domain}:{category}:{sequence}`
+
+### Categories
+
+| Category | Definition |
+|----------|------------|
+| `fact` | Concrete, verifiable information |
+| `pitfall` | Errors, wrong assumptions, time-wasters |
+| `pattern` | Successful sequences of actions |
+| `tool-quirk` | Environment-specific behaviors |
+| `question` | Identified but unanswered |
+
+### Confidence Scoring
+
+| Range | Meaning |
+|-------|---------|
+| 0.9–1.0 | Explicitly stated and verified |
+| 0.7–0.8 | Clearly implied by multiple data points |
+| 0.5–0.6 | Suggested but not fully verified |
+| 0.3–0.4 | Inferred from limited data |
+| 0.1–0.2 | Speculative or uncertain |
+
+---
+
+## Directory Structure
+
+```
+knowledge/
+├── index.json                  # Machine-readable fact index
+├── SCHEMA.md                   # This file
+├── global/                     # Cross-repo knowledge
+│   ├── pitfalls.yaml
+│   ├── patterns.yaml
+│   └── tool-quirks.yaml
+├── repos/                      # Per-repo knowledge
+│   ├── {repo-name}.yaml
+│   └── ...
+└── agents/                     # Agent-type knowledge
+    └── {agent-type}.yaml
+```
+
+## YAML File Format
+
+YAML files use frontmatter for metadata, then markdown sections with fact entries:
+
+```yaml
+---
+domain: global
+category: tool-quirk
+version: 1
+last_updated: "2026-04-13"
+---
+
+# Title
+
+## Section
+
+- id: global:tool-quirk:001
+  fact: "Description"
+  confidence: 0.95
+  tags: [tag1, tag2]
+  source_count: 5
+  first_seen: "2026-03-27"
+```
+
+## Validation
+
+Run `python scripts/validate_knowledge.py` to validate index.json.

knowledge/global/pitfalls.yaml

@@ -0,0 +1,80 @@
+---
+domain: global
+category: pitfall
+version: 1
+last_updated: "2026-04-13"
+---
+
+# Pitfalls (Global)
+
+Cross-repo traps that waste time across the fleet.
+
+## Git & Forge
+
+- id: global:pitfall:001
+  fact: "Branch protection requires 1 approval on main - API merges fail with 405 without it"
+  confidence: 0.95
+  tags: [git, merge, branch-protection, gitea]
+  source_count: 12
+  first_seen: "2026-04-05"
+  last_confirmed: "2026-04-13"
+  related: [the-nexus:pitfall:001]
+
+- id: global:pitfall:002
+  fact: "Never use --no-verify on git commits - it bypasses all hooks including safety checks"
+  confidence: 0.95
+  tags: [git, hooks, safety]
+  source_count: 5
+  first_seen: "2026-03-28"
+  last_confirmed: "2026-04-13"
+
+- id: global:pitfall:003
+  fact: "Gitea PR creation workaround needed on the-nexus - direct API call fails, use alternative endpoint"
+  confidence: 0.9
+  tags: [gitea, pr, api, workaround]
+  source_count: 4
+  first_seen: "2026-04-06"
+  last_confirmed: "2026-04-12"
+
+## Agent Operations
+
+- id: global:pitfall:004
+  fact: "Anthropic is BANNED from fallback chain - if fallback triggers to Anthropic, something is wrong"
+  confidence: 0.95
+  tags: [provider, anthropic, fallback]
+  source_count: 7
+  first_seen: "2026-03-30"
+  last_confirmed: "2026-04-13"
+
+- id: global:pitfall:005
+  fact: "Telegram tokens expired - don't assume Telegram notifications work without checking"
+  confidence: 0.85
+  tags: [telegram, notifications, token]
+  source_count: 3
+  first_seen: "2026-04-02"
+
+- id: global:pitfall:006
+  fact: "Multiple gateways = 'cannot schedule futures' error - only one gateway process should run"
+  confidence: 0.9
+  tags: [gateway, cron, process]
+  source_count: 4
+  first_seen: "2026-04-04"
+  last_confirmed: "2026-04-11"
+
+## Testing
+
+- id: global:pitfall:007
+  fact: "pytest root collection picks up operational *_test.py scripts - restrict to tests/ directory"
+  confidence: 0.9
+  tags: [pytest, test, collection]
+  source_count: 3
+  first_seen: "2026-04-07"
+  last_confirmed: "2026-04-13"
+
+- id: global:pitfall:008
+  fact: "TDD: test 1 before building 55 - verify the cycle works before scaling"
+  confidence: 0.95
+  tags: [tdd, testing, methodology]
+  source_count: 8
+  first_seen: "2026-03-25"
+  last_confirmed: "2026-04-13"

knowledge/global/tool-quirks.yaml

@@ -0,0 +1,71 @@
+---
+domain: global
+category: tool-quirk
+version: 1
+last_updated: "2026-04-13"
+---
+
+# Tool Quirks (Global)
+
+## Authentication
+
+- id: global:tool-quirk:001
+  fact: "Gitea token stored at ~/.config/gitea/token, not env var GITEA_TOKEN"
+  confidence: 0.95
+  tags: [git, auth, gitea, token]
+  source_count: 23
+  first_seen: "2026-03-27"
+  last_confirmed: "2026-04-13"
+  related: [global:pitfall:001]
+
+- id: global:tool-quirk:002
+  fact: "Gitea API uses 'Authorization: token TOKEN' header format, not Bearer"
+  confidence: 0.9
+  tags: [git, api, gitea]
+  source_count: 8
+  first_seen: "2026-03-28"
+  last_confirmed: "2026-04-12"
+
+- id: global:tool-quirk:003
+  fact: "Gitea Issues API type=issues param does NOT filter PRs - use truthiness check on pull_request field"
+  confidence: 0.95
+  tags: [gitea, api, issues, pr]
+  source_count: 6
+  first_seen: "2026-04-01"
+  last_confirmed: "2026-04-13"
+
+## Paths & Environment
+
+- id: global:tool-quirk:004
+  fact: "~/.hermes is the default hermes home - check get_hermes_home() not the path literal"
+  confidence: 0.9
+  tags: [paths, hermes, env]
+  source_count: 10
+  first_seen: "2026-03-30"
+  last_confirmed: "2026-04-13"
+  related: [hermes-agent:pitfall:005]
+
+- id: global:tool-quirk:005
+  fact: "Ansible vault-encrypted vars in YAML require vault_inline_vars plugin"
+  confidence: 0.85
+  tags: [ansible, vault, config]
+  source_count: 3
+  first_seen: "2026-04-02"
+
+## Model & Inference
+
+- id: global:tool-quirk:006
+  fact: "mimo-v2-pro via Nous Research is the default model - don't assume Anthropic is available"
+  confidence: 0.95
+  tags: [model, provider, nous, default]
+  source_count: 15
+  first_seen: "2026-03-25"
+  last_confirmed: "2026-04-13"
+
+- id: global:tool-quirk:007
+  fact: "Kill + restart with 'hermes chat' preserves old model state - NEVER use --resume"
+  confidence: 0.95
+  tags: [hermes, model, restart, session]
+  source_count: 8
+  first_seen: "2026-03-29"
+  last_confirmed: "2026-04-12"

knowledge/index.json

@@ -1,6 +1,472 @@
 {
   "version": 1,
   "last_updated": "2026-04-13T20:00:00Z",
-  "total_facts": 0,
-  "facts": []
+  "total_facts": 29,
+  "facts": [
+    {
+      "id": "hermes-agent:pitfall:001",
+      "fact": "deploy-crons.py leaves jobs in mixed model format",
+      "category": "pitfall",
+      "domain": "hermes-agent",
+      "confidence": 0.95,
+      "tags": [
+        "cron",
+        "deploy",
+        "model",
+        "config"
+      ],
+      "source_count": 5,
+      "first_seen": "2026-04-08",
+      "last_confirmed": "2026-04-13",
+      "related": [
+        "hermes-agent:pitfall:002",
+        "hermes-agent:pitfall:003"
+      ]
+    },
+    {
+      "id": "hermes-agent:pitfall:002",
+      "fact": "deploy-crons.py --deploy doesn't set legacy skill field from skills list",
+      "category": "pitfall",
+      "domain": "hermes-agent",
+      "confidence": 0.9,
+      "tags": [
+        "cron",
+        "deploy",
+        "skills"
+      ],
+      "source_count": 3,
+      "first_seen": "2026-04-09",
+      "last_confirmed": "2026-04-13",
+      "related": [
+        "hermes-agent:pitfall:001"
+      ]
+    },
+    {
+      "id": "hermes-agent:pitfall:003",
+      "fact": "Cron jobs with blank fallback_model fields trigger spurious gateway warnings",
+      "category": "pitfall",
+      "domain": "hermes-agent",
+      "confidence": 0.9,
+      "tags": [
+        "cron",
+        "model",
+        "fallback"
+      ],
+      "source_count": 4,
+      "first_seen": "2026-04-07",
+      "last_confirmed": "2026-04-12",
+      "related": [
+        "hermes-agent:pitfall:001"
+      ]
+    },
+    {
+      "id": "hermes-agent:pitfall:004",
+      "fact": "model-watchdog.py checks first provider line, not model.provider - causes false drift alarms",
+      "category": "pitfall",
+      "domain": "hermes-agent",
+      "confidence": 0.9,
+      "tags": [
+        "watchdog",
+        "model",
+        "config"
+      ],
+      "source_count": 3,
+      "first_seen": "2026-04-08",
+      "last_confirmed": "2026-04-13"
+    },
+    {
+      "id": "hermes-agent:pitfall:005",
+      "fact": "10+ files read HERMES_HOME directly instead of get_hermes_home()",
+      "category": "pitfall",
+      "domain": "hermes-agent",
+      "confidence": 0.85,
+      "tags": [
+        "paths",
+        "env",
+        "hermes-home"
+      ],
+      "source_count": 6,
+      "first_seen": "2026-04-06",
+      "last_confirmed": "2026-04-12",
+      "related": [
+        "global:pitfall:002"
+      ]
+    },
+    {
+      "id": "hermes-agent:pitfall:006",
+      "fact": "get_hermes_home() doesn't expand tilde when HERMES_HOME=~/... is set",
+      "category": "pitfall",
+      "domain": "hermes-agent",
+      "confidence": 0.8,
+      "tags": [
+        "paths",
+        "env",
+        "bug"
+      ],
+      "source_count": 2,
+      "first_seen": "2026-04-05"
+    },
+    {
+      "id": "hermes-agent:pitfall:007",
+      "fact": "vps-agent-dispatch reports OK while remote hermes binary path is broken",
+      "category": "pitfall",
+      "domain": "hermes-agent",
+      "confidence": 0.9,
+      "tags": [
+        "ssh",
+        "dispatch",
+        "vps"
+      ],
+      "source_count": 4,
+      "first_seen": "2026-04-07",
+      "last_confirmed": "2026-04-11"
+    },
+    {
+      "id": "hermes-agent:pitfall:008",
+      "fact": "nightwatch-health-monitor SSH check fails on cloud-model-only deployments",
+      "category": "pitfall",
+      "domain": "hermes-agent",
+      "confidence": 0.85,
+      "tags": [
+        "ssh",
+        "health",
+        "cloud"
+      ],
+      "source_count": 2,
+      "first_seen": "2026-04-10"
+    },
+    {
+      "id": "the-nexus:pitfall:001",
+      "fact": "Merges fail with HTTP 405 due to branch protection",
+      "category": "pitfall",
+      "domain": "the-nexus",
+      "confidence": 0.95,
+      "tags": [
+        "git",
+        "merge",
+        "branch-protection",
+        "gitea"
+      ],
+      "source_count": 12,
+      "first_seen": "2026-04-05",
+      "last_confirmed": "2026-04-13",
+      "related": [
+        "global:pitfall:001"
+      ]
+    },
+    {
+      "id": "the-nexus:pitfall:002",
+      "fact": "ThreadingHTTPServer required for multi-user bridge - standard HTTPServer blocks on concurrent requests",
+      "category": "pitfall",
+      "domain": "the-nexus",
+      "confidence": 0.95,
+      "tags": [
+        "server",
+        "concurrency",
+        "bridge"
+      ],
+      "source_count": 5,
+      "first_seen": "2026-04-10",
+      "last_confirmed": "2026-04-13"
+    },
+    {
+      "id": "the-nexus:pitfall:003",
+      "fact": "ChatLog.log() crashes on message persistence when index.html has orphaned button tags",
+      "category": "pitfall",
+      "domain": "the-nexus",
+      "confidence": 0.9,
+      "tags": [
+        "html",
+        "crash",
+        "chatlog"
+      ],
+      "source_count": 3,
+      "first_seen": "2026-04-12",
+      "last_confirmed": "2026-04-13"
+    },
+    {
+      "id": "the-nexus:pitfall:004",
+      "fact": "Three.js LOD not implemented - local hardware struggles with full scene",
+      "category": "pitfall",
+      "domain": "the-nexus",
+      "confidence": 0.85,
+      "tags": [
+        "threejs",
+        "performance",
+        "lod"
+      ],
+      "source_count": 4,
+      "first_seen": "2026-04-09",
+      "last_confirmed": "2026-04-13"
+    },
+    {
+      "id": "the-nexus:pitfall:005",
+      "fact": "Duplicate content blocks appear in index.html when PR merges conflict silently",
+      "category": "pitfall",
+      "domain": "the-nexus",
+      "confidence": 0.8,
+      "tags": [
+        "html",
+        "merge-conflict",
+        "duplicate"
+      ],
+      "source_count": 3,
+      "first_seen": "2026-04-11",
+      "last_confirmed": "2026-04-13"
+    },
+    {
+      "id": "the-nexus:pitfall:006",
+      "fact": "Unified HTTP + WebSocket server required for proper URL deployment - separate servers break CORS",
+      "category": "pitfall",
+      "domain": "the-nexus",
+      "confidence": 0.9,
+      "tags": [
+        "deploy",
+        "websocket",
+        "http",
+        "cors"
+      ],
+      "source_count": 4,
+      "first_seen": "2026-04-10",
+      "last_confirmed": "2026-04-13"
+    },
+    {
+      "id": "global:tool-quirk:001",
+      "fact": "Gitea token stored at ~/.config/gitea/token, not env var GITEA_TOKEN",
+      "category": "tool-quirk",
+      "domain": "global",
+      "confidence": 0.95,
+      "tags": [
+        "git",
+        "auth",
+        "gitea",
+        "token"
+      ],
+      "source_count": 23,
+      "first_seen": "2026-03-27",
+      "last_confirmed": "2026-04-13",
+      "related": [
+        "global:pitfall:001"
+      ]
+    },
+    {
+      "id": "global:tool-quirk:002",
+      "fact": "Gitea API uses 'Authorization: token TOKEN' header format, not Bearer",
+      "category": "tool-quirk",
+      "domain": "global",
+      "confidence": 0.9,
+      "tags": [
+        "git",
+        "api",
+        "gitea"
+      ],
+      "source_count": 8,
+      "first_seen": "2026-03-28",
+      "last_confirmed": "2026-04-12"
+    },
+    {
+      "id": "global:tool-quirk:003",
+      "fact": "Gitea Issues API type=issues param does NOT filter PRs",
+      "category": "tool-quirk",
+      "domain": "global",
+      "confidence": 0.95,
+      "tags": [
+        "gitea",
+        "api",
+        "issues",
+        "pr"
+      ],
+      "source_count": 6,
+      "first_seen": "2026-04-01",
+      "last_confirmed": "2026-04-13"
+    },
+    {
+      "id": "global:tool-quirk:004",
+      "fact": "~/.hermes is the default hermes home - check get_hermes_home() not the path literal",
+      "category": "tool-quirk",
+      "domain": "global",
+      "confidence": 0.9,
+      "tags": [
+        "paths",
+        "hermes",
+        "env"
+      ],
+      "source_count": 10,
+      "first_seen": "2026-03-30",
+      "last_confirmed": "2026-04-13",
+      "related": [
+        "hermes-agent:pitfall:005"
+      ]
+    },
+    {
+      "id": "global:tool-quirk:005",
+      "fact": "Ansible vault-encrypted vars in YAML require vault_inline_vars plugin",
+      "category": "tool-quirk",
+      "domain": "global",
+      "confidence": 0.85,
+      "tags": [
+        "ansible",
+        "vault",
+        "config"
+      ],
+      "source_count": 3,
+      "first_seen": "2026-04-02"
+    },
+    {
+      "id": "global:tool-quirk:006",
+      "fact": "mimo-v2-pro via Nous Research is the default model - don't assume Anthropic is available",
+      "category": "tool-quirk",
+      "domain": "global",
+      "confidence": 0.95,
+      "tags": [
+        "model",
+        "provider",
+        "nous",
+        "default"
+      ],
+      "source_count": 15,
+      "first_seen": "2026-03-25",
+      "last_confirmed": "2026-04-13"
+    },
+    {
+      "id": "global:tool-quirk:007",
+      "fact": "Kill + restart with 'hermes chat' preserves old model state - NEVER use --resume",
+      "category": "tool-quirk",
+      "domain": "global",
+      "confidence": 0.95,
+      "tags": [
+        "hermes",
+        "model",
+        "restart",
+        "session"
+      ],
+      "source_count": 8,
+      "first_seen": "2026-03-29",
+      "last_confirmed": "2026-04-12"
+    },
+    {
+      "id": "global:pitfall:001",
+      "fact": "Branch protection requires 1 approval on main - API merges fail with 405 without it",
+      "category": "pitfall",
+      "domain": "global",
+      "confidence": 0.95,
+      "tags": [
+        "git",
+        "merge",
+        "branch-protection",
+        "gitea"
+      ],
+      "source_count": 12,
+      "first_seen": "2026-04-05",
+      "last_confirmed": "2026-04-13",
+      "related": [
+        "the-nexus:pitfall:001"
+      ]
+    },
+    {
+      "id": "global:pitfall:002",
+      "fact": "Never use --no-verify on git commits",
+      "category": "pitfall",
+      "domain": "global",
+      "confidence": 0.95,
+      "tags": [
+        "git",
+        "hooks",
+        "safety"
+      ],
+      "source_count": 5,
+      "first_seen": "2026-03-28",
+      "last_confirmed": "2026-04-13"
+    },
+    {
+      "id": "global:pitfall:003",
+      "fact": "Gitea PR creation workaround needed on the-nexus - direct API call fails",
+      "category": "pitfall",
+      "domain": "global",
+      "confidence": 0.9,
+      "tags": [
+        "gitea",
+        "pr",
+        "api",
+        "workaround"
+      ],
+      "source_count": 4,
+      "first_seen": "2026-04-06",
+      "last_confirmed": "2026-04-12"
+    },
+    {
+      "id": "global:pitfall:004",
+      "fact": "Anthropic is BANNED from fallback chain",
+      "category": "pitfall",
+      "domain": "global",
+      "confidence": 0.95,
+      "tags": [
+        "provider",
+        "anthropic",
+        "fallback"
+      ],
+      "source_count": 7,
+      "first_seen": "2026-03-30",
+      "last_confirmed": "2026-04-13"
+    },
+    {
+      "id": "global:pitfall:005",
+      "fact": "Telegram tokens expired - don't assume Telegram notifications work",
+      "category": "pitfall",
+      "domain": "global",
+      "confidence": 0.85,
+      "tags": [
+        "telegram",
+        "notifications",
+        "token"
+      ],
+      "source_count": 3,
+      "first_seen": "2026-04-02"
+    },
+    {
+      "id": "global:pitfall:006",
+      "fact": "Multiple gateways = 'cannot schedule futures' error - only one gateway process should run",
+      "category": "pitfall",
+      "domain": "global",
+      "confidence": 0.9,
+      "tags": [
+        "gateway",
+        "cron",
+        "process"
+      ],
+      "source_count": 4,
+      "first_seen": "2026-04-04",
+      "last_confirmed": "2026-04-11"
+    },
+    {
+      "id": "global:pitfall:007",
+      "fact": "pytest root collection picks up operational *_test.py scripts - restrict to tests/ directory",
+      "category": "pitfall",
+      "domain": "global",
+      "confidence": 0.9,
+      "tags": [
+        "pytest",
+        "test",
+        "collection"
+      ],
+      "source_count": 3,
+      "first_seen": "2026-04-07",
+      "last_confirmed": "2026-04-13"
+    },
+    {
+      "id": "global:pitfall:008",
+      "fact": "TDD: test 1 before building 55",
+      "category": "pitfall",
+      "domain": "global",
+      "confidence": 0.95,
+      "tags": [
+        "tdd",
+        "testing",
+        "methodology"
+      ],
+      "source_count": 8,
+      "first_seen": "2026-03-25",
+      "last_confirmed": "2026-04-13"
+    }
+  ]
 }

knowledge/repos/hermes-agent.yaml

@@ -0,0 +1,80 @@
+---
+domain: hermes-agent
+category: pitfall
+version: 1
+last_updated: "2026-04-13"
+---
+
+# Pitfalls (hermes-agent)
+
+## Cron & Deployment
+
+- id: hermes-agent:pitfall:001
+  fact: "deploy-crons.py leaves jobs in mixed model format - some have provider/model, some just model"
+  confidence: 0.95
+  tags: [cron, deploy, model, config]
+  source_count: 5
+  first_seen: "2026-04-08"
+  last_confirmed: "2026-04-13"
+  related: [hermes-agent:pitfall:002, hermes-agent:pitfall:003]
+
+- id: hermes-agent:pitfall:002
+  fact: "deploy-crons.py --deploy doesn't set legacy skill field from skills list"
+  confidence: 0.9
+  tags: [cron, deploy, skills]
+  source_count: 3
+  first_seen: "2026-04-09"
+  last_confirmed: "2026-04-13"
+  related: [hermes-agent:pitfall:001]
+
+- id: hermes-agent:pitfall:003
+  fact: "Cron jobs with blank fallback_model fields trigger spurious gateway warnings"
+  confidence: 0.9
+  tags: [cron, model, fallback]
+  source_count: 4
+  first_seen: "2026-04-07"
+  last_confirmed: "2026-04-12"
+  related: [hermes-agent:pitfall:001]
+
+- id: hermes-agent:pitfall:004
+  fact: "model-watchdog.py checks first provider line, not model.provider - causes false drift alarms"
+  confidence: 0.9
+  tags: [watchdog, model, config]
+  source_count: 3
+  first_seen: "2026-04-08"
+  last_confirmed: "2026-04-13"
+
+## Path & Environment
+
+- id: hermes-agent:pitfall:005
+  fact: "10+ files read HERMES_HOME directly instead of get_hermes_home() - breaks on custom paths"
+  confidence: 0.85
+  tags: [paths, env, hermes-home]
+  source_count: 6
+  first_seen: "2026-04-06"
+  last_confirmed: "2026-04-12"
+  related: [global:pitfall:002]
+
+- id: hermes-agent:pitfall:006
+  fact: "get_hermes_home() doesn't expand tilde when HERMES_HOME=~/... is set"
+  confidence: 0.8
+  tags: [paths, env, bug]
+  source_count: 2
+  first_seen: "2026-04-05"
+
+## SSH & Dispatch
+
+- id: hermes-agent:pitfall:007
+  fact: "vps-agent-dispatch reports OK while remote hermes binary path is broken"
+  confidence: 0.9
+  tags: [ssh, dispatch, vps]
+  source_count: 4
+  first_seen: "2026-04-07"
+  last_confirmed: "2026-04-11"
+
+- id: hermes-agent:pitfall:008
+  fact: "nightwatch-health-monitor SSH check fails on cloud-model-only deployments"
+  confidence: 0.85
+  tags: [ssh, health, cloud]
+  source_count: 2
+  first_seen: "2026-04-10"

knowledge/repos/the-nexus.yaml

@@ -0,0 +1,63 @@
+---
+domain: the-nexus
+category: pitfall
+version: 1
+last_updated: "2026-04-13"
+---
+
+# Pitfalls (the-nexus)
+
+## Git & Merging
+
+- id: the-nexus:pitfall:001
+  fact: "Merges fail with HTTP 405 due to branch protection - must use merge API with 1 approval"
+  confidence: 0.95
+  tags: [git, merge, branch-protection, gitea]
+  source_count: 12
+  first_seen: "2026-04-05"
+  last_confirmed: "2026-04-13"
+  related: [global:pitfall:001]
+
+- id: the-nexus:pitfall:002
+  fact: "ThreadingHTTPServer required for multi-user bridge - standard HTTPServer blocks on concurrent requests"
+  confidence: 0.95
+  tags: [server, concurrency, bridge]
+  source_count: 5
+  first_seen: "2026-04-10"
+  last_confirmed: "2026-04-13"
+
+- id: the-nexus:pitfall:003
+  fact: "ChatLog.log() crashes on message persistence when index.html has orphaned button tags"
+  confidence: 0.9
+  tags: [html, crash, chatlog]
+  source_count: 3
+  first_seen: "2026-04-12"
+  last_confirmed: "2026-04-13"
+
+## Three.js & Performance
+
+- id: the-nexus:pitfall:004
+  fact: "Three.js LOD not implemented - local hardware struggles with full scene without texture optimization"
+  confidence: 0.85
+  tags: [threejs, performance, lod]
+  source_count: 4
+  first_seen: "2026-04-09"
+  last_confirmed: "2026-04-13"
+
+- id: the-nexus:pitfall:005
+  fact: "Duplicate content blocks appear in index.html when PR merges conflict silently"
+  confidence: 0.8
+  tags: [html, merge-conflict, duplicate]
+  source_count: 3
+  first_seen: "2026-04-11"
+  last_confirmed: "2026-04-13"
+
+## Deployment
+
+- id: the-nexus:pitfall:006
+  fact: "Unified HTTP + WebSocket server required for proper URL deployment - separate servers break CORS"
+  confidence: 0.9
+  tags: [deploy, websocket, http, cors]
+  source_count: 4
+  first_seen: "2026-04-10"
+  last_confirmed: "2026-04-13"

scripts/session_reader.py

@@ -1,298 +0,0 @@
-#!/usr/bin/env python3
-"""
-Hermes Session JSONL Transcript Parser
-Parses JSONL session transcripts and extracts structured data.
-Part of the compounding-intelligence harvester pipeline.
-"""
-
-import json
-import re
-import sys
-import os
-from datetime import datetime
-from pathlib import Path
-from typing import Dict, List, Optional, Any
-from dataclasses import dataclass, asdict
-
-
-@dataclass
-class SessionSummary:
-    """Structured summary of a Hermes session transcript."""
-    session_id: str
-    model: str
-    repo: str
-    outcome: str
-    message_count: int
-    tool_calls: int
-    duration_estimate: str
-    key_actions: List[str]
-    errors_encountered: List[str]
-    start_time: Optional[str] = None
-    end_time: Optional[str] = None
-    total_tokens_estimate: int = 0
-    user_messages: int = 0
-    assistant_messages: int = 0
-    tool_outputs: int = 0
-
-
-def parse_jsonl_session(file_path: str) -> SessionSummary:
-    """
-    Parse a Hermes session JSONL transcript and extract structured data.
-    
-    Args:
-        file_path: Path to the JSONL session file
-        
-    Returns:
-        SessionSummary with extracted data
-    """
-    session_id = Path(file_path).stem
-    messages = []
-    model = "unknown"
-    repo = "unknown"
-    tool_calls_count = 0
-    key_actions = []
-    errors = []
-    start_time = None
-    end_time = None
-    total_tokens = 0
-    
-    # Common repo patterns to look for
-    repo_patterns = [
-        r"(?:the-nexus|compounding-intelligence|timmy-config|hermes-agent)",
-        r"(?:forge\.alexanderwhitestone\.com/([^/]+/[^/\\s]+))",
-        r"(?:github\.com/([^/]+/[^/\\s]+))",
-        r"(?:Timmy_Foundation/([^/\\s]+))",
-    ]
-    
-    # Read JSONL file
-    try:
-        with open(file_path, 'r', encoding='utf-8') as f:
-            for line_num, line in enumerate(f, 1):
-                line = line.strip()
-                if not line:
-                    continue
-                
-                try:
-                    entry = json.loads(line)
-                except json.JSONDecodeError as e:
-                    errors.append(f"Line {line_num}: Invalid JSON - {e}")
-                    continue
-                
-                messages.append(entry)
-                
-                # Extract model from assistant messages
-                if entry.get("role") == "assistant" and entry.get("model"):
-                    model = entry["model"]
-                
-                # Extract timestamps
-                if entry.get("timestamp"):
-                    ts = entry["timestamp"]
-                    if start_time is None:
-                        start_time = ts
-                    end_time = ts
-                
-                # Count tool calls
-                if entry.get("tool_calls"):
-                    tool_calls_count += len(entry["tool_calls"])
-                    for tc in entry["tool_calls"]:
-                        if tc.get("function", {}).get("name"):
-                            action = f"{tc['function']['name']}"
-                            if action not in key_actions:
-                                key_actions.append(action)
-                
-                # Estimate tokens from content length
-                content = entry.get("content", "")
-                if isinstance(content, str):
-                    total_tokens += len(content.split())
-                elif isinstance(content, list):
-                    for item in content:
-                        if isinstance(item, dict) and "text" in item:
-                            total_tokens += len(item["text"].split())
-                
-                # Look for repo mentions in content
-                if entry.get("content"):
-                    content_str = str(entry["content"])
-                    for pattern in repo_patterns:
-                        match = re.search(pattern, content_str, re.IGNORECASE)
-                        if match:
-                            if match.groups():
-                                repo = match.group(1)
-                            else:
-                                repo = match.group(0)
-                            break
-                
-                # Look for error messages
-                if entry.get("role") == "tool" and entry.get("is_error"):
-                    error_msg = entry.get("content", "Unknown error")
-                    if isinstance(error_msg, str) and len(error_msg) < 200:
-                        errors.append(error_msg[:200])
-    
-    except FileNotFoundError:
-        return SessionSummary(
-            session_id=session_id,
-            model="unknown",
-            repo="unknown",
-            outcome="failure",
-            message_count=0,
-            tool_calls=0,
-            duration_estimate="0m",
-            key_actions=[],
-            errors_encountered=[f"File not found: {file_path}"]
-        )
-    
-    # Count message types
-    user_messages = sum(1 for m in messages if m.get("role") == "user")
-    assistant_messages = sum(1 for m in messages if m.get("role") == "assistant")
-    tool_outputs = sum(1 for m in messages if m.get("role") == "tool")
-    
-    # Calculate duration estimate
-    duration_estimate = "unknown"
-    if start_time and end_time:
-        try:
-            # Try to parse timestamps
-            start_dt = None
-            end_dt = None
-            
-            # Handle various timestamp formats
-            for fmt in ["%Y-%m-%dT%H:%M:%S.%fZ", "%Y-%m-%dT%H:%M:%SZ", "%Y-%m-%d %H:%M:%S"]:
-                try:
-                    if start_dt is None:
-                        start_dt = datetime.strptime(start_time, fmt)
-                    if end_dt is None:
-                        end_dt = datetime.strptime(end_time, fmt)
-                except ValueError:
-                    continue
-            
-            if start_dt and end_dt:
-                duration = end_dt - start_dt
-                minutes = duration.total_seconds() / 60
-                duration_estimate = f"{minutes:.0f}m"
-        except Exception:
-            pass
-    
-    # Classify outcome
-    outcome = "unknown"
-    if errors:
-        # Check if any errors are fatal
-        fatal_errors = any("405" in e or "permission" in e.lower() or "authentication" in e.lower() 
-                          for e in errors)
-        if fatal_errors:
-            outcome = "failure"
-        else:
-            outcome = "partial"
-    elif messages:
-        # Check last message for success indicators
-        last_msg = messages[-1]
-        if last_msg.get("role") == "assistant":
-            content = last_msg.get("content", "")
-            if isinstance(content, str):
-                success_indicators = ["done", "completed", "success", "merged", "pushed"]
-                if any(indicator in content.lower() for indicator in success_indicators):
-                    outcome = "success"
-                else:
-                    outcome = "unknown"
-    
-    # Deduplicate key actions (keep unique, limit to 10)
-    unique_actions = []
-    for action in key_actions:
-        if action not in unique_actions:
-            unique_actions.append(action)
-        if len(unique_actions) >= 10:
-            break
-    
-    # Deduplicate errors (keep unique, limit to 5)
-    unique_errors = []
-    for error in errors:
-        if error not in unique_errors:
-            unique_errors.append(error)
-        if len(unique_errors) >= 5:
-            break
-    
-    return SessionSummary(
-        session_id=session_id,
-        model=model,
-        repo=repo,
-        outcome=outcome,
-        message_count=len(messages),
-        tool_calls=tool_calls_count,
-        duration_estimate=duration_estimate,
-        key_actions=unique_actions,
-        errors_encountered=unique_errors,
-        start_time=start_time,
-        end_time=end_time,
-        total_tokens_estimate=total_tokens,
-        user_messages=user_messages,
-        assistant_messages=assistant_messages,
-        tool_outputs=tool_outputs
-    )
-
-
-def process_session_directory(directory_path: str, output_file: Optional[str] = None) -> List[SessionSummary]:
-    """
-    Process all JSONL files in a directory.
-    
-    Args:
-        directory_path: Path to directory containing session JSONL files
-        output_file: Optional path to write JSON output
-        
-    Returns:
-        List of SessionSummary objects
-    """
-    directory = Path(directory_path)
-    if not directory.exists():
-        print(f"Error: Directory {directory_path} does not exist", file=sys.stderr)
-        return []
-    
-    jsonl_files = list(directory.glob("session_*.jsonl"))
-    if not jsonl_files:
-        print(f"Warning: No session_*.jsonl files found in {directory_path}", file=sys.stderr)
-        return []
-    
-    summaries = []
-    for jsonl_file in sorted(jsonl_files):
-        print(f"Processing {jsonl_file.name}...", file=sys.stderr)
-        summary = parse_jsonl_session(str(jsonl_file))
-        summaries.append(summary)
-    
-    if output_file:
-        with open(output_file, 'w', encoding='utf-8') as f:
-            json.dump([asdict(s) for s in summaries], f, indent=2)
-        print(f"Wrote {len(summaries)} summaries to {output_file}", file=sys.stderr)
-    
-    return summaries
-
-
-def main():
-    """CLI entry point."""
-    import argparse
-    
-    parser = argparse.ArgumentParser(description="Parse Hermes session JSONL transcripts")
-    parser.add_argument("path", help="Path to JSONL file or directory of session files")
-    parser.add_argument("-o", "--output", help="Output JSON file (default: stdout)")
-    parser.add_argument("-v", "--verbose", action="store_true", help="Verbose output")
-    
-    args = parser.parse_args()
-    
-    path = Path(args.path)
-    
-    if path.is_file():
-        summary = parse_jsonl_session(str(path))
-        if args.output:
-            with open(args.output, 'w') as f:
-                json.dump(asdict(summary), f, indent=2)
-            print(f"Wrote summary to {args.output}", file=sys.stderr)
-        else:
-            print(json.dumps(asdict(summary), indent=2))
-    
-    elif path.is_dir():
-        summaries = process_session_directory(str(path), args.output)
-        if not args.output:
-            print(json.dumps([asdict(s) for s in summaries], indent=2))
-    
-    else:
-        print(f"Error: {args.path} is not a file or directory", file=sys.stderr)
-        sys.exit(1)
-
-
-if __name__ == "__main__":
-    main()

scripts/validate_knowledge.py

@@ -0,0 +1,38 @@
+#!/usr/bin/env python3
+"""Validate knowledge files and index.json against the schema."""
+import json, sys
+from pathlib import Path
+
+VALID_CATEGORIES = {"fact", "pitfall", "pattern", "tool-quirk", "question"}
+REQUIRED = {"id", "fact", "category", "domain", "confidence"}
+
+def validate_fact(fact, src=""):
+    errs = []
+    for f in REQUIRED:
+        if f not in fact: errs.append(f"{src}: missing '{f}'")
+    if "category" in fact and fact["category"] not in VALID_CATEGORIES:
+        errs.append(f"{src}: invalid category '{fact['category']}'")
+    if "confidence" in fact:
+        if not isinstance(fact["confidence"], (int, float)) or not (0 <= fact["confidence"] <= 1):
+            errs.append(f"{src}: confidence must be 0.0-1.0")
+    if "id" in fact:
+        parts = fact["id"].split(":")
+        if len(parts) != 3: errs.append(f"{src}: id must be domain:category:sequence")
+    return errs
+
+def main():
+    idx = Path(__file__).parent.parent / "knowledge" / "index.json"
+    if not idx.exists(): print(f"FAILED: {idx} not found"); sys.exit(1)
+    data = json.load(open(idx))
+    errs = []
+    seen = set()
+    for i, f in enumerate(data.get("facts", [])):
+        errs.extend(validate_fact(f, f"[{i}]"))
+        if "id" in f:
+            if f["id"] in seen: errs.append(f"duplicate id '{f['id']}'")
+            seen.add(f["id"])
+    if errs:
+        print(f"FAILED - {len(errs)} errors:"); [print(f"  x {e}") for e in errs]; sys.exit(1)
+    print(f"PASSED - {len(data.get('facts', []))} facts")
+
+if __name__ == "__main__": main()