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 → ~/.llm-wiki/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.

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.

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 vault's category folders — the rows of the CATEGORIES table in AGENTS.md (or categories from llm-wiki layout --json) — in table order, so colors are stable across runs: the first row gets palette index 0, the second index 1, and so on. A standard vault gets:

Folders added by roles take the earlier indexes because they come first in the table. A vault without a CATEGORIES table uses the original seven folders, in the order llm-wiki layout prints. With more than 10 folders, cap at 10 and tell the user the rest share the "other" color.

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

{"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)

{"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:

   {
     "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 indent — preserve what's there).

Step 4: Report and Log

Print a summary like:

Graph colorized → .obsidian/graph.json
  Mode:    by-tag
  Groups:  7 color assignments
  Palette: blue, orange, red, teal, green, yellow, purple
  Backup:  .obsidian/graph.json.backup-20260424-1432

Reload Obsidian (Cmd/Ctrl+R) to see the new colors.
If Obsidian is currently open, close it first OR reload immediately — Obsidian
overwrites graph.json on close and can erase these changes.

Append to $VAULT_PATH/log.md:

- [TIMESTAMP] GRAPH_COLORIZE mode=<mode> groups=<N> backup=graph.json.backup-<stamp>

Edge Cases

• No tags in vault in by-tag mode → fall back to by-category and tell the user.
• User wants to undo → restore from the latest graph.json.backup-* and note that in log.md.
• User wants to clear all color groups → set colorGroups: [], back up, log as GRAPH_COLORIZE mode=clear.
• .obsidian/ missing → the vault hasn't been opened in Obsidian yet. Tell the user to open it once, then re-run. Don't create .obsidian/ yourself — Obsidian populates many files there on first open.
• Query syntax gotchas: folder paths with spaces need quoting (path:"my folder"); tags with nested slashes work literally (tag:#visibility/internal); don't URL-encode.
• Obsidian open during edit: surface the risk — Obsidian reads graph.json at startup and rewrites it on close. If the user is editing live, tell them to close Obsidian first or run the reload (Cmd/Ctrl+R) immediately and avoid opening graph settings before they do.

Notes

• This is a pure config edit — no page content changes, no frontmatter writes.
• Re-running is safe: each run creates a new backup, only colorGroups is rewritten.
• If the user has manually curated color groups they want to keep, offer combined mode or ask before overwriting.
• The palette here matches wiki-export's graph.html community colors, so the Obsidian graph and the exported visualization look consistent.