Graph ColorizeCAUTION

Framework for AI agents to build and maintain a digital brain through Obsidian wiki | Memory System for Agents

The instruction file, verbatim from the audited commit — this is the text the model reads, and the surface the audit's instruction layer examines. Quoted here so you can judge it without cloning anything.

---
name: graph-colorize
description: >
  Configure Obsidian graph colors by tag, folder, category, or visibility by updating .obsidian/graph.json. Use for graph colorization; preserve other graph settings and back up before changes.
---

# Graph Colorize — Color-code the Obsidian Graph View

You are rewriting `$OBSIDIAN_VAULT_PATH/.obsidian/graph.json` so Obsidian's graph view tints nodes by tag, folder, or visibility.

Obsidian stores graph settings in `<vault>/.obsidian/graph.json`. The `colorGroups` array is a list of `{query, color}` pairs; the first matching query wins per node. Queries use Obsidian's search syntax: `tag:#foo`, `path:"concepts"`, `file:foo`, etc. Color is `{"a": 1, "rgb": <packed-int>}` where the int is `(R << 16) | (G << 8) | B`.

## Before You Start

1. **Resolve config** — follow the Config Resolution Protocol in `llm-wiki/SKILL.md` (inline `@name` override → walk up CWD for `.env` → global config → prompt setup). This gives `OBSIDIAN_VAULT_PATH`.
2. Confirm `$OBSIDIAN_VAULT_PATH/.obsidian/` exists. If it doesn't, the vault has never been opened in Obsidian — tell the user to open the vault once in Obsidian, then re-run.
3. **Warn the user if Obsidian is likely open**: Obsidian overwrites `graph.json` on close. Tell them to close the vault first, or be ready to reload (Cmd/Ctrl+R) and not touch the graph settings until they reload.

## Step 1: Pick a Mode

Infer the mode from the user's phrasing. If ambiguous, default to **by-tag**.

| User intent | Mode |
|---|---|
| "color by tag", "color my graph", "make it colorful" (default) | `by-tag` |
| "color by folder", "color by category", "color by directory" | `by-category` |
| "highlight visibility", "show internal/pii in graph", "visibility colors" | `by-visibility` |
| User provides explicit mapping (`tag:#foo = red`, or JSON blob) | `custom` |
| "combine tag and visibility" / "both" | `combined` (visibility first, then tag) |

## Step 2: Build the `colorGroups` Array

### Palette (10 distinct, colorblind-friendly colors)

Use in order. If more groups than colors, cycle and add a lightness shift by dividing brightness ~20% via a second pass — or just cap at 10 and tell the user the remaining tags share the "other" color.

| # | Hex | rgb (packed int) | Role |
|---|---|---|---|
| 0 | `#4E79A7` | `5142951` | blue |
| 1 | `#F28E2B` | `15896107` | orange |
| 2 | `#E15759` | `14767961` | red |
| 3 | `#76B7B2` | `7780786` | teal |
| 4 | `#59A14F` | `5873999` | green |
| 5 | `#EDC948` | `15583048` | yellow |
| 6 | `#B07AA1` | `11565217` | purple |
| 7 | `#FF9DA7` | `16751527` | pink |
| 8 | `#9C755F` | `10253663` | brown |
| 9 | `#BAB0AC` | `12234924` | gray |

Every color is wrapped as `{"a": 1, "rgb": <int>}`.

### Mode: `by-tag`

1. Glob `$VAULT_PATH/**/*.md` excluding `_archives/`, `_raw/`, `.obsidian/`, `node_modules/`, `index.md`, `log.md`, `_insights.md`.
2. Parse frontmatter `tags` from each page. Count usage per tag.
3. **Drop `visibility/*` tags** from the frequency list — they are reserved system tags, handled only in `by-visibility` or `combined` mode.
4. Take the top 10 tags by usage. If there are fewer than 10 unique tags, use all of them.
5. For each tag `T` at index `i`: emit `{"query": "tag:#T", "color": palette[i]}`.
6. Optionally, append a final catch-all entry for untagged pages at the end: `{"query": "-[\"tag\":]", "color": palette[9]}` — **skip** if color slot 9 is already taken by a real tag.

### Mode: `by-category`

Use the seven vault top-level folders in this fixed order so colors are stable across runs:

| Folder | Color index |
|---|---|
| `concepts` | 0 (blue) |
| `entities` | 1 (orange) |
| `skills` | 2 (red) |
| `references` | 3 (teal) |
| `synthesis` | 4 (green) |
| `projects` | 5 (yellow) |
| `journal` | 6 (purple) |

Emit one entry per folder that exists AND contains at least one `.md` file. Each entry is:

```json
{"query": "path:\"<folder>\"", "color": {"a": 1, "rgb": <int>}}
```

### Mode: `by-visibility`

Emit exactly three entries, in this order (first-match wins, so most restrictive comes first):

1. `visibility/pii` → `#E15759` (red, rgb 14767961)
2. `visibility/internal` → `#F28E2B` (orange, rgb 15896107)
3. `visibility/public` → `#59A14F` (green, rgb 5873999)

```json
{"query": "tag:#visibility/pii", "color": {"a": 1, "rgb": 14767961}}
```

Pages with no `visibility/` tag remain Obsidian's default color — do not add a catch-all.

### Mode: `combined`

Emit `by-visibility` entries first, then `by-tag` entries. Visibility wins on conflict because it appears first in the list.

### Mode: `custom`

If the user gave explicit mappings, honor them literally. Convert any hex they give (e.g. `#FF00FF`) to packed int using `int(hex_without_hash, 16)`. Wrap each as `{"a": 1, "rgb": <int>}`.

## Step 3: Merge into graph.json (Do Not Clobber)

1. Read the existing `$VAULT_PATH/.obsidian/graph.json`. If it doesn't exist, start from this minimal default:

   ```json
   {
     "collapse-filter": true,
     "search": "",
     "showTags": false,
     "showAttachments": false,
     "hideUnresolved": false,
     "showOrphans": true,
     "collapse-color-groups": false,
     "colorGroups": [],
     "collapse-display": true,
     "showArrow": false,
     "textFadeMultiplier": 0,
     "nodeSizeMultiplier": 1,
     "lineSizeMultiplier": 1,
     "collapse-forces": true,
     "centerStrength": 0.518713248970312,
     "repelStrength": 10,
     "linkStrength": 1,
     "linkDistance": 250,
     "scale": 1,
     "close": true
   }
   ```

2. **Back up first**: copy the existing file to `.obsidian/graph.json.backup-<YYYYMMDD-HHMM>` before writing. If a backup from the same minute exists, reuse it — don't pile up duplicates.

3. Replace **only** the `colorGroups` field with your new array. Leave every other field untouched. This preserves the user's zoom, physics, filter, search, and display preferences.

4. Write the file back with the same JSON style as the original (usually compact single-line or 2-space 

CAUTIONgrade B · trust 89/100 Install with care. The audit found things worth knowing before you trust its output.

What the source does

Filesystem

none-observed

Network

none-observed

Shell

none-observed

Dependencies

pinned

Secrets in source

none-found

Findings (5)

.agents/skills/claude-history-ingest

.agents/skills/code-understand

.agents/skills/codex-history-ingest

.agents/skills/copilot-history-ingest

.agents/skills/cross-linker

Gates applied: no_behavioural_pass.

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