better-dsh 0.2.5-c → 0.2.5-e

package/docs/80_upstream-docs-and-skills/hermes-dev-skill/src/docs/user-guide/skills/bundled/research/research-llm-wiki.md

@@ -1,526 +0,0 @@
----
-title: "Llm Wiki — Karpathy's LLM Wiki: build/query interlinked markdown KB"
-sidebar_label: "Llm Wiki"
-description: "Karpathy's LLM Wiki: build/query interlinked markdown KB"
----
-
-{/* This page is auto-generated from the skill's SKILL.md by website/scripts/generate-skill-docs.py. Edit the source SKILL.md, not this page. */}
-
-# Llm Wiki
-
-Karpathy's LLM Wiki: build/query interlinked markdown KB.
-
-## Skill metadata
-
-| | |
-|---|---|
-| Source | Bundled (installed by default) |
-| Path | `skills/research\llm-wiki` |
-| Version | `2.1.0` |
-| Author | Hermes Agent |
-| License | MIT |
-| Platforms | linux, macos, windows |
-| Tags | `wiki`, `knowledge-base`, `research`, `notes`, `markdown`, `rag-alternative` |
-| Related skills | [`obsidian`](/docs/user-guide/skills/bundled/note-taking/note-taking-obsidian), [`arxiv`](/docs/user-guide/skills/bundled/research/research-arxiv) |
-
-## Reference: full SKILL.md
-
-:::info
-The following is the complete skill definition that Hermes loads when this skill is triggered. This is what the agent sees as instructions when the skill is active.
-:::
-
-# Karpathy's LLM Wiki
-
-Build and maintain a persistent, compounding knowledge base as interlinked markdown files.
-Based on [Andrej Karpathy's LLM Wiki pattern](https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f).
-
-Unlike traditional RAG (which rediscovers knowledge from scratch per query), the wiki
-compiles knowledge once and keeps it current. Cross-references are already there.
-Contradictions have already been flagged. Synthesis reflects everything ingested.
-
-**Division of labor:** The human curates sources and directs analysis. The agent
-summarizes, cross-references, files, and maintains consistency.
-
-## When This Skill Activates
-
-Use this skill when the user:
-- Asks to create, build, or start a wiki or knowledge base
-- Asks to ingest, add, or process a source into their wiki
-- Asks a question and an existing wiki is present at the configured path
-- Asks to lint, audit, or health-check their wiki
-- References their wiki, knowledge base, or "notes" in a research context
-
-## Wiki Location
-
-**Location:** Set via `WIKI_PATH` environment variable (e.g. in `${HERMES_HOME:-~/.hermes}/.env`).
-
-If unset, defaults to `~/wiki`.
-
-```bash
-WIKI="${WIKI_PATH:-$HOME/wiki}"
-```
-
-The wiki is just a directory of markdown files — open it in Obsidian, VS Code, or
-any editor. No database, no special tooling required.
-
-## Architecture: Three Layers
-
-<!-- ascii-guard-ignore -->
-```
-wiki/
-├── SCHEMA.md           # Conventions, structure rules, domain config
-├── index.md            # Sectioned content catalog with one-line summaries
-├── log.md              # Chronological action log (append-only, rotated yearly)
-├── raw/                # Layer 1: Immutable source material
-│   ├── articles/       # Web articles, clippings
-│   ├── papers/         # PDFs, arxiv papers
-│   ├── transcripts/    # Meeting notes, interviews
-│   └── assets/         # Images, diagrams referenced by sources
-├── entities/           # Layer 2: Entity pages (people, orgs, products, models)
-├── concepts/           # Layer 2: Concept/topic pages
-├── comparisons/        # Layer 2: Side-by-side analyses
-└── queries/            # Layer 2: Filed query results worth keeping
-```
-<!-- ascii-guard-ignore-end -->
-
-**Layer 1 — Raw Sources:** Immutable. The agent reads but never modifies these.
-**Layer 2 — The Wiki:** Agent-owned markdown files. Created, updated, and
-cross-referenced by the agent.
-**Layer 3 — The Schema:** `SCHEMA.md` defines structure, conventions, and tag taxonomy.
-
-## Resuming an Existing Wiki (CRITICAL — do this every session)
-
-When the user has an existing wiki, **always orient yourself before doing anything**:
-
-① **Read `SCHEMA.md`** — understand the domain, conventions, and tag taxonomy.
-② **Read `index.md`** — learn what pages exist and their summaries.
-③ **Scan recent `log.md`** — read the last 20-30 entries to understand recent activity.
-
-```bash
-WIKI="${WIKI_PATH:-$HOME/wiki}"
-# Orientation reads at session start
-read_file "$WIKI/SCHEMA.md"
-read_file "$WIKI/index.md"
-read_file "$WIKI/log.md" offset=<last 30 lines>
-```
-
-Only after orientation should you ingest, query, or lint. This prevents:
-- Creating duplicate pages for entities that already exist
-- Missing cross-references to existing content
-- Contradicting the schema's conventions
-- Repeating work already logged
-
-For large wikis (100+ pages), also run a quick `search_files` for the topic
-at hand before creating anything new.
-
-## Initializing a New Wiki
-
-When the user asks to create or start a wiki:
-
-1. Determine the wiki path (from `$WIKI_PATH` env var, or ask the user; default `~/wiki`)
-2. Create the directory structure above
-3. Ask the user what domain the wiki covers — be specific
-4. Write `SCHEMA.md` customized to the domain (see template below)
-5. Write initial `index.md` with sectioned header
-6. Write initial `log.md` with creation entry
-7. Confirm the wiki is ready and suggest first sources to ingest
-
-### SCHEMA.md Template
-
-Adapt to the user's domain. The schema constrains agent behavior and ensures consistency:
-
-```markdown
-# Wiki Schema
-
-## Domain
-[What this wiki covers — e.g., "AI/ML research", "personal health", "startup intelligence"]
-
-## Conventions
-- File names: lowercase, hyphens, no spaces (e.g., `transformer-architecture.md`)
-- Every wiki page starts with YAML frontmatter (see below)
-- Use `[[wikilinks]]` to link between pages (minimum 2 outbound links per page)
-- When updating a page, always bump the `updated` date
-- Every new page must be added to `index.md` under the correct section
-- Every action must be appended to `log.md`
-- **Provenance markers:** On pages that synthesize 3+ sources, append `^[raw/articles/source-file.md]`
-  at the end of paragraphs whose claims come from a specific source. This lets a reader trace each
-  claim back without re-reading the whole raw file. Optional on single-source pages where the
-  `sources:` frontmatter is enough.
-
-## Frontmatter
-  ```yaml
-  ---
-  title: Page Title
-  created: YYYY-MM-DD
-  updated: YYYY-MM-DD
-  type: entity | concept | comparison | query | summary
-  tags: [from taxonomy below]
-  sources: [raw/articles/source-name.md]
-  # Optional quality signals:
-  confidence: high | medium | low        # how well-supported the claims are
-  contested: true                        # set when the page has unresolved contradictions
-  contradictions: [other-page-slug]      # pages this one conflicts with
-  ---
-  ```
-
-`confidence` and `contested` are optional but recommended for opinion-heavy or fast-moving
-topics. Lint surfaces `contested: true` and `confidence: low` pages for review so weak claims
-don't silently harden into accepted wiki fact.
-
-### raw/ Frontmatter
-
-Raw sources ALSO get a small frontmatter block so re-ingests can detect drift:
-
-```yaml
----
-source_url: https://example.com/article   # original URL, if applicable
-ingested: YYYY-MM-DD
-sha256: &lt;hex digest of the raw content below the frontmatter>
----
-```
-
-The `sha256:` lets a future re-ingest of the same URL skip processing when content is unchanged,
-and flag drift when it has changed. Compute over the body only (everything after the closing
-`---`), not the frontmatter itself.
-
-## Tag Taxonomy
-[Define 10-20 top-level tags for the domain. Add new tags here BEFORE using them.]
-
-Example for AI/ML:
-- Models: model, architecture, benchmark, training
-- People/Orgs: person, company, lab, open-source
-- Techniques: optimization, fine-tuning, inference, alignment, data
-- Meta: comparison, timeline, controversy, prediction
-
-Rule: every tag on a page must appear in this taxonomy. If a new tag is needed,
-add it here first, then use it. This prevents tag sprawl.
-
-## Page Thresholds
-- **Create a page** when an entity/concept appears in 2+ sources OR is central to one source
-- **Add to existing page** when a source mentions something already covered
-- **DON'T create a page** for passing mentions, minor details, or things outside the domain
-- **Split a page** when it exceeds ~200 lines — break into sub-topics with cross-links
-- **Archive a page** when its content is fully superseded — move to `_archive/`, remove from index
-
-## Entity Pages
-One page per notable entity. Include:
-- Overview / what it is
-- Key facts and dates
-- Relationships to other entities ([[wikilinks]])
-- Source references
-
-## Concept Pages
-One page per concept or topic. Include:
-- Definition / explanation
-- Current state of knowledge
-- Open questions or debates
-- Related concepts ([[wikilinks]])
-
-## Comparison Pages
-Side-by-side analyses. Include:
-- What is being compared and why
-- Dimensions of comparison (table format preferred)
-- Verdict or synthesis
-- Sources
-
-## Update Policy
-When new information conflicts with existing content:
-1. Check the dates — newer sources generally supersede older ones
-2. If genuinely contradictory, note both positions with dates and sources
-3. Mark the contradiction in frontmatter: `contradictions: [page-name]`
-4. Flag for user review in the lint report
-```
-
-### index.md Template
-
-The index is sectioned by type. Each entry is one line: wikilink + summary.
-
-```markdown
-# Wiki Index
-
-> Content catalog. Every wiki page listed under its type with a one-line summary.
-> Read this first to find relevant pages for any query.
-> Last updated: YYYY-MM-DD | Total pages: N
-
-## Entities
-<!-- Alphabetical within section -->
-
-## Concepts
-
-## Comparisons
-
-## Queries
-```
-
-**Scaling rule:** When any section exceeds 50 entries, split it into sub-sections
-by first letter or sub-domain. When the index exceeds 200 entries total, create
-a `_meta/topic-map.md` that groups pages by theme for faster navigation.
-
-### log.md Template
-
-```markdown
-# Wiki Log
-
-> Chronological record of all wiki actions. Append-only.
-> Format: `## [YYYY-MM-DD] action | subject`
-> Actions: ingest, update, query, lint, create, archive, delete
-> When this file exceeds 500 entries, rotate: rename to log-YYYY.md, start fresh.
-
-## [YYYY-MM-DD] create | Wiki initialized
-- Domain: [domain]
-- Structure created with SCHEMA.md, index.md, log.md
-```
-
-## Core Operations
-
-### 1. Ingest
-
-When the user provides a source (URL, file, paste), integrate it into the wiki:
-
-① **Capture the raw source:**
-   - URL → use `web_extract` to get markdown, save to `raw/articles/`
-   - PDF → use `web_extract` (handles PDFs), save to `raw/papers/`
-   - Pasted text → save to appropriate `raw/` subdirectory
-   - Name the file descriptively: `raw/articles/karpathy-llm-wiki-2026.md`
-   - **Add raw frontmatter** (`source_url`, `ingested`, `sha256` of the body).
-     On re-ingest of the same URL: recompute the sha256, compare to the stored value —
-     skip if identical, flag drift and update if different. This is cheap enough to
-     do on every re-ingest and catches silent source changes.
-
-② **Discuss takeaways** with the user — what's interesting, what matters for
-   the domain. (Skip this in automated/cron contexts — proceed directly.)
-
-③ **Check what already exists** — search index.md and use `search_files` to find
-   existing pages for mentioned entities/concepts. This is the difference between
-   a growing wiki and a pile of duplicates.
-
-④ **Write or update wiki pages:**
-   - **New entities/concepts:** Create pages only if they meet the Page Thresholds
-     in SCHEMA.md (2+ source mentions, or central to one source)
-   - **Existing pages:** Add new information, update facts, bump `updated` date.
-     When new info contradicts existing content, follow the Update Policy.
-   - **Cross-reference:** Every new or updated page must link to at least 2 other
-     pages via `[[wikilinks]]`. Check that existing pages link back.
-   - **Tags:** Only use tags from the taxonomy in SCHEMA.md
-   - **Provenance:** On pages synthesizing 3+ sources, append `^[raw/articles/source.md]`
-     markers to paragraphs whose claims trace to a specific source.
-   - **Confidence:** For opinion-heavy, fast-moving, or single-source claims, set
-     `confidence: medium` or `low` in frontmatter. Don't mark `high` unless the
-     claim is well-supported across multiple sources.
-
-⑤ **Update navigation:**
-   - Add new pages to `index.md` under the correct section, alphabetically
-   - Update the "Total pages" count and "Last updated" date in index header
-   - Append to `log.md`: `## [YYYY-MM-DD] ingest | Source Title`
-   - List every file created or updated in the log entry
-
-⑥ **Report what changed** — list every file created or updated to the user.
-
-A single source can trigger updates across 5-15 wiki pages. This is normal
-and desired — it's the compounding effect.
-
-### 2. Query
-
-When the user asks a question about the wiki's domain:
-
-① **Read `index.md`** to identify relevant pages.
-② **For wikis with 100+ pages**, also `search_files` across all `.md` files
-   for key terms — the index alone may miss relevant content.
-③ **Read the relevant pages** using `read_file`.
-④ **Synthesize an answer** from the compiled knowledge. Cite the wiki pages
-   you drew from: "Based on [[page-a]] and [[page-b]]..."
-⑤ **File valuable answers back** — if the answer is a substantial comparison,
-   deep dive, or novel synthesis, create a page in `queries/` or `comparisons/`.
-   Don't file trivial lookups — only answers that would be painful to re-derive.
-⑥ **Update log.md** with the query and whether it was filed.
-
-### 3. Lint
-
-When the user asks to lint, health-check, or audit the wiki:
-
-① **Orphan pages:** Find pages with no inbound `[[wikilinks]]` from other pages.
-```python
-# Use execute_code for this — programmatic scan across all wiki pages
-import os, re
-from collections import defaultdict
-wiki = "<WIKI_PATH>"
-# Scan all .md files in entities/, concepts/, comparisons/, queries/
-# Extract all [[wikilinks]] — build inbound link map
-# Pages with zero inbound links are orphans
-```
-
-② **Broken wikilinks:** Find `[[links]]` that point to pages that don't exist.
-
-③ **Index completeness:** Every wiki page should appear in `index.md`. Compare
-   the filesystem against index entries.
-
-④ **Frontmatter validation:** Every wiki page must have all required fields
-   (title, created, updated, type, tags, sources). Tags must be in the taxonomy.
-
-⑤ **Stale content:** Pages whose `updated` date is >90 days older than the most
-   recent source that mentions the same entities.
-
-⑥ **Contradictions:** Pages on the same topic with conflicting claims. Look for
-   pages that share tags/entities but state different facts. Surface all pages
-   with `contested: true` or `contradictions:` frontmatter for user review.
-
-⑦ **Quality signals:** List pages with `confidence: low` and any page that cites
-   only a single source but has no confidence field set — these are candidates
-   for either finding corroboration or demoting to `confidence: medium`.
-
-⑧ **Source drift:** For each file in `raw/` with a `sha256:` frontmatter, recompute
-   the hash and flag mismatches. Mismatches indicate the raw file was edited
-   (shouldn't happen — raw/ is immutable) or ingested from a URL that has since
-   changed. Not a hard error, but worth reporting.
-
-⑨ **Page size:** Flag pages over 200 lines — candidates for splitting.
-
-⑩ **Tag audit:** List all tags in use, flag any not in the SCHEMA.md taxonomy.
-
-⑪ **Log rotation:** If log.md exceeds 500 entries, rotate it.
-
-⑫ **Report findings** with specific file paths and suggested actions, grouped by
-   severity (broken links > orphans > source drift > contested pages > stale content > style issues).
-
-⑬ **Append to log.md:** `## [YYYY-MM-DD] lint | N issues found`
-
-## Working with the Wiki
-
-### Searching
-
-```bash
-# Find pages by content
-search_files "transformer" path="$WIKI" file_glob="*.md"
-
-# Find pages by filename
-search_files "*.md" target="files" path="$WIKI"
-
-# Find pages by tag
-search_files "tags:.*alignment" path="$WIKI" file_glob="*.md"
-
-# Recent activity
-read_file "$WIKI/log.md" offset=<last 20 lines>
-```
-
-### Bulk Ingest
-
-When ingesting multiple sources at once, batch the updates:
-1. Read all sources first
-2. Identify all entities and concepts across all sources
-3. Check existing pages for all of them (one search pass, not N)
-4. Create/update pages in one pass (avoids redundant updates)
-5. Update index.md once at the end
-6. Write a single log entry covering the batch
-
-### Archiving
-
-When content is fully superseded or the domain scope changes:
-1. Create `_archive/` directory if it doesn't exist
-2. Move the page to `_archive/` with its original path (e.g., `_archive/entities/old-page.md`)
-3. Remove from `index.md`
-4. Update any pages that linked to it — replace wikilink with plain text + "(archived)"
-5. Log the archive action
-
-### Obsidian Integration
-
-The wiki directory works as an Obsidian vault out of the box:
-- `[[wikilinks]]` render as clickable links
-- Graph View visualizes the knowledge network
-- YAML frontmatter powers Dataview queries
-- The `raw/assets/` folder holds images referenced via `![[image.png]]`
-
-For best results:
-- Set Obsidian's attachment folder to `raw/assets/`
-- Enable "Wikilinks" in Obsidian settings (usually on by default)
-- Install Dataview plugin for queries like `TABLE tags FROM "entities" WHERE contains(tags, "company")`
-
-If using the Obsidian skill alongside this one, set `OBSIDIAN_VAULT_PATH` to the
-same directory as the wiki path.
-
-### Obsidian Headless (servers and headless machines)
-
-On machines without a display, use `obsidian-headless` instead of the desktop app.
-It syncs vaults via Obsidian Sync without a GUI — perfect for agents running on
-servers that write to the wiki while Obsidian desktop reads it on another device.
-
-**Setup:**
-```bash
-# Requires Node.js 22+
-npm install -g obsidian-headless
-
-# Login (requires Obsidian account with Sync subscription)
-ob login --email <email> --password '<password>'
-
-# Create a remote vault for the wiki
-ob sync-create-remote --name "LLM Wiki"
-
-# Connect the wiki directory to the vault
-cd ~/wiki
-ob sync-setup --vault "<vault-id>"
-
-# Initial sync
-ob sync
-
-# Continuous sync (foreground — use systemd for background)
-ob sync --continuous
-```
-
-**Continuous background sync via systemd:**
-```ini
-# ~/.config/systemd/user/obsidian-wiki-sync.service
-[Unit]
-Description=Obsidian LLM Wiki Sync
-After=network-online.target
-Wants=network-online.target
-
-[Service]
-ExecStart=/path/to/ob sync --continuous
-WorkingDirectory=%h/wiki
-Restart=on-failure
-RestartSec=10
-
-[Install]
-WantedBy=default.target
-```
-
-```bash
-systemctl --user daemon-reload
-systemctl --user enable --now obsidian-wiki-sync
-# Enable linger so sync survives logout:
-sudo loginctl enable-linger $USER
-```
-
-This lets the agent write to `~/wiki` on a server while you browse the same
-vault in Obsidian on your laptop/phone — changes appear within seconds.
-
-## Pitfalls
-
-- **Never modify files in `raw/`** — sources are immutable. Corrections go in wiki pages.
-- **Always orient first** — read SCHEMA + index + recent log before any operation in a new session.
-  Skipping this causes duplicates and missed cross-references.
-- **Always update index.md and log.md** — skipping this makes the wiki degrade. These are the
-  navigational backbone.
-- **Don't create pages for passing mentions** — follow the Page Thresholds in SCHEMA.md. A name
-  appearing once in a footnote doesn't warrant an entity page.
-- **Don't create pages without cross-references** — isolated pages are invisible. Every page must
-  link to at least 2 other pages.
-- **Frontmatter is required** — it enables search, filtering, and staleness detection.
-- **Tags must come from the taxonomy** — freeform tags decay into noise. Add new tags to SCHEMA.md
-  first, then use them.
-- **Keep pages scannable** — a wiki page should be readable in 30 seconds. Split pages over
-  200 lines. Move detailed analysis to dedicated deep-dive pages.
-- **Ask before mass-updating** — if an ingest would touch 10+ existing pages, confirm
-  the scope with the user first.
-- **Rotate the log** — when log.md exceeds 500 entries, rename it `log-YYYY.md` and start fresh.
-  The agent should check log size during lint.
-- **Handle contradictions explicitly** — don't silently overwrite. Note both claims with dates,
-  mark in frontmatter, flag for user review.
-
-## Related Tools
-
-[llm-wiki-compiler](https://github.com/atomicmemory/llm-wiki-compiler) is a Node.js CLI that
-compiles sources into a concept wiki with the same Karpathy inspiration. It's Obsidian-compatible,
-so users who want a scheduled/CLI-driven compile pipeline can point it at the same vault this
-skill maintains. Trade-offs: it owns page generation (replaces the agent's judgment on page
-creation) and is tuned for small corpora. Use this skill when you want agent-in-the-loop curation;
-use llmwiki when you want batch compile of a source directory.