Updated Skills: DisMech (markdown)
8500849
docs: move tech-recon to core skills
tech-recon lives in skills/ (core), not in alhazen-skill-examples (external).
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
64d5e64
docs: complete wiki rewrite for April 2026
Rewrites all public-facing wiki documentation to reflect current state:
New pages:
- Gap-Architecture.md: full gap detection, filing, fix, and PR workflow
- Skills:-Scientific-Literature.md: 4 sources, 8 commands, schema
- Skills:-ALG-Precision-Therapeutics.md: rare disease investigation
- Skills:-Literature-Trends.md: hypothesis genealogy skill
- Skills:-They-Said-Whaaa.md: credibility/consistency tracker
- Skills:-DisMech.md: DisMech disease mechanism KB (750+ diseases)
- Skills:-Tech-Recon.md: 7-phase technology investigation
- Skills:-Web-Search.md: SearXNG usage
- Skills:-Curation-Skill-Builder.md: 6-phase design framework
Rewrites:
- Home.md: core vs external skills tables, all 10 skills, 3-mode deployment
- Skill-Architecture.md: SKILL.md/USAGE.md split, skills-registry.yaml,
TypeDB 3.x conventions, gap-driven evolution
- Design-Concepts.md: 6-phase framework, full schema hierarchy, gap-first design
- Schema-Reference.md: core hierarchy, attributes, relations, namespace table,
TypeDB 3.x syntax guide
- Getting-Started.md: make build flow, verification steps, troubleshooting
- Deployment.md: deploy.sh A->B->C ladder, stack components, known issues
- _Sidebar.md: restructured into Getting Started / Architecture /
Core Skills / Domain Skills / Links
- Skills:-TypeDB-Notebook.md: updated integration section
Archived (notices added, originals preserved):
- Skills:-Domain-Modeling.md -> Skills:-Curation-Skill-Builder.md
- Skills:-Rare-Disease.md -> ALG-Precision-Therapeutics + DisMech
- OpenClaw-Configuration.md -> Deployment.md
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
1438d33
docs: change 'Notebook memory' to 'ontological memory'
a49e47b
User edits: rename interface section, extend History closing line
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
5cfd952
Add Skills: Domain Modeling wiki page
Meta-skill guide covering: when domain modeling is warranted, the
central design question (work backwards from the queries you want),
placing concepts in the 3-branch hierarchy, TypeQL schema conventions,
the sensemaking provenance chain, SKILL.md vs USAGE.md authoring
guidance, Python script conventions, common pitfalls, and pointers
to jobhunt and rare-disease as reference implementations.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
9731663
Add section on Ibn al-Haytham's obscurity in the Western tradition
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
43956e4
Add USAGE.md to Skill-Architecture documentation
Document the SKILL.md/USAGE.md split: SKILL.md is kept short and
loaded at startup; USAGE.md contains full workflow instructions and
is loaded on demand. Updated diagram, component table, section headers,
SKILL.md/USAGE.md structure templates, checklist, and template listing.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
693c865
Document SKILL.md vs USAGE.md split in Design Concepts
Explain why skills use two instruction files: SKILL.md is loaded into
OpenClaw's system context at startup (must stay short), USAGE.md is
loaded on demand when executing the skill (full instructions).
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
25d71c7
Replace generic 'Claude' with 'Agent' throughout wiki
Systematically replaced uses of 'Claude' that serve as a proxy for
the generic agentic interface with 'Agent'. Preserved 'Claude Code'
(product name), 'Claude, Goose, OpenClaw' (platform lists), and
model/API-specific references (tool use, model selection).
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
d0e9bb6
Remove Deployment:-Mac-Mini-Native.md and clean up references
- Delete Deployment:-Mac-Mini-Native.md
- _Sidebar.md: remove Mac Mini Native entry
- Getting-Started.md: point Stage B row directly to [[Deployment]]
- Deployment.md: remove two cross-references to the deleted page
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
bf6727e
Add prototype disclaimer to Home.md
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
052e9aa
Remove experimental skill pages and clean up all references
Deleted pages:
- Skills:-APM.md, Skills:-EPMC-Search.md, Skills:-TechRecon.md
- Skills:-Domain-Modeling.md
- Schema:-Precision-Medicine.md, Schema:-Scientific-Literature.md
- Schema:-Tech-Recon.md
Reference cleanup:
- _Sidebar.md: remove deleted skills from Experimental Skills section;
remove Scientific Literature, Precision Medicine, Tech Recon from Schema
- Schema-Reference.md: remove deleted namespace rows from table
- Skill-Architecture.md: remove EPMC Search, APM, Domain Modeling examples
- Skills:-TypeDB-Notebook.md: replace EPMC Search + Domain Modeling bullets
with Rare Disease
- Skills:-Rare-Disease.md: remove APM cross-skill integration section;
reframe philosophy section without APM dependency
- Design-Concepts.md: rewrite APM/rare-disease cross-namespace example to
reference only rare-disease
- Dashboard-Organization.md: remove TechRecon route group, components/
techrecon entry, and Related link
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
2658e77
docs(deployment): update for deploy.env + make targets + macos-native
- Primary interface is now deploy.env + make deploy-macmini/deploy-vps
- Add deploy.env variable table with DEPLOY_BRANCH explanation
- Add deploy.env Variable column to deploy.sh options table
- Fix Ansible dispatcher: Darwin → macos-native.yml (not container-deploy.yml)
- Add macos-native.yml to playbook file tree
- Fix Directory Layout: separate macOS native (~/.openclaw/) from VPS container (openclaw-docker/)
- Fix Telegram Setup paths per platform
- Fix Updating Skills: replace stale cp command with update-skills.sh
- Fix Troubleshooting: correct Skills not found path for macOS native
- Getting Started: split OpenClaw into B (Mac Mini) and C (VPS)
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
2b7c1cf
Update Home.md framing and structure
- Tighten 'What is Alhazen?' to emphasize notebook memory
- Add 'Why Skillful?' section explaining skills as a design choice
and linking to the alhazen-skill-examples repository
- Rename 'System Organization' to clarify the three layers (Agent,
TypeDB, Skills) with expanded Skills description
- Relabel production skills table as 'Demonstration Skills'
- Minor prose cleanup throughout
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
e58c693
Add SVG block diagram for container stack architecture
Replace ASCII art in Deployment.md with a colour-coded SVG showing
the full 7-service container network: Telegram → OpenClaw → LiteLLM
→ Anthropic API, OpenClaw → TypeDB / MCP Server / Dashboard, and
MCP Server → Squid Proxy → allowlisted domains. Dashed lines mark
connections that cross into the external zone.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
076b830
Update deployment docs to align with two-mode framing
- Deployment.md: connect intro to two-mode framing; name jobhunt forager
and rare-disease as the primary production use cases; fix Stage A command
to match Getting-Started (make db-start && claude); add link to Getting
Started for Stage A context
- Deployment:-Mac-Mini-Native.md: replace hardcoded 'gullyburns' user
references with generic '<your-user>'; sharpen intro to situate page as
Stage B of A→B→C journey; call out jobhunt forager as the primary
production workflow enabled by this setup
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
db1ec79
Reframe wiki around Claude Code + OpenClaw; add rare-disease skill docs
- Rewrite Home.md: two-mode architecture, featured vs experimental skills,
TypeDB domain modeling callout, overnight forager quick example
- Update Getting-Started.md: A→B→C workflow table, rare-disease example,
replace EPMC Search with rare-disease
- New Skills:-Rare-Disease.md: 5-phase workflow, all commands, sensemaking
workflows, TypeDB schema highlights, NGLY1 end-to-end example
- Expand Skills:-Jobhunt.md: automated forager, 7-step sensemaking workflow,
TypeDB schema from source, OpenClaw cron config, full command tables
- Add TypeDB domain modeling section to Design-Concepts.md: schema-first
design, 3-branch hierarchy guide, cross-namespace query examples
- Restructure _Sidebar.md: Skills vs Experimental Skills hierarchy
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
6c985c1
Ran a security audit and documented implementation fixes here
8d5c746
Add OpenClaw Configuration wiki page (gateway, cron, Tailscale Serve)
08a4544
Update Schema Reference with v2 hierarchy diagram
Replace old ICE/research-item Mermaid diagram with the three-branch
identifiable-entity hierarchy showing domain-thing, collection, and
information-content-entity branches.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
92fd3a4
Fix stale research-item in query example
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
f852592
Update Design Concepts for v2 schema hierarchy
Reflect identifiable-entity/domain-thing/ICE split in schema
vocabulary section and data model section. Add typed collections
explanation and link to Schema Reference.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
817d356
Update schema docs for v2 hierarchy restructuring
Reflects identifiable-entity/domain-thing/ICE split:
- identifiable-entity as abstract root
- domain-thing replaces research-item
- Typed collections per namespace
- Attribute redistribution
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
37f7d22
Use horizontal layout for class diagrams
Add direction LR to all Mermaid class diagrams so type
hierarchies read left-to-right instead of top-to-bottom.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
edc25d4
Fix Mermaid rendering: escape 'note' reserved keyword
Mermaid treats 'note' as a reserved keyword, causing parse errors
in class and ER diagrams. Renamed to 'note_t' in diagram output.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
0fb1dd6
Merge branch 'master' of https://github.com/GullyBurns/skillful-alhazen.wiki
4e582c1
Added TypeDB documentation
7979055