Obsidian

Obsidian Vault

Use this skill for filesystem-first Obsidian vault work: reading notes, listing notes, searching note files, creating notes, appending content, and adding wikilinks. For the specific pattern of exporting an agent's skill library as interlinked MOC notes, see references/hermes-skill-catalog-pattern.md.

Vault path

Use a known or resolved vault path before calling file tools.

The documented vault-path convention is the OBSIDIAN_VAULT_PATH environment variable, for example from ${HERMES_HOME:-~/.hermes}/.env. If it is unset, use ~/Documents/Obsidian Vault.

File tools do not expand shell variables. Do not pass paths containing $OBSIDIAN_VAULT_PATH to read_file, write_file, patch, or search_files; resolve the vault path first and pass a concrete absolute path. Vault paths may contain spaces, which is another reason to prefer file tools over shell commands.

If the vault path is unknown, terminal is acceptable for resolving OBSIDIAN_VAULT_PATH or checking whether the fallback path exists. Once the path is known, switch back to file tools.

Read a note

Use read_file with the resolved absolute path to the note. Prefer this over cat because it provides line numbers and pagination.

List notes

Use search_files with target: "files" and the resolved vault path. Prefer this over find or ls.

• To list all markdown notes, use pattern: "*.md" under the vault path.
• To list a subfolder, search under that subfolder's absolute path.

Search

Use search_files for both filename and content searches. Prefer this over grep, find, or ls.

• For filenames, use search_files with target: "files" and a filename pattern.
• For note contents, use search_files with target: "content", the content regex as pattern, and file_glob: "*.md" when you want to restrict matches to markdown notes.

Create a note

Use write_file with the resolved absolute path and the full markdown content. Prefer this over shell heredocs or echo because it avoids shell quoting issues and returns structured results.

Append to a note

Prefer a native file-tool workflow when it is not awkward:

• Read the target note with read_file.
• Use patch for an anchored append when there is stable context, such as adding a section after an existing heading or appending before a known trailing block.
• Use write_file when rewriting the whole note is clearer than constructing a fragile patch.

For an anchored append with patch, replace the anchor with the anchor plus the new content.

For a simple append with no stable context, terminal is acceptable if it is the clearest safe option.

Targeted edits

Use patch for focused note changes when the current content gives you stable context. Prefer this over shell text rewriting.

Wikilinks

Obsidian links notes with [[Note Name]] syntax. When creating notes, use these to link related content.

When deleting or renaming notes, always search for remaining wikilinks pointing to the old name and fix them. Use search_files with target: "content" and a regex like \[\[Old Name(\||\]\]) to find all references, then patch each one.

Vault cleanup

When asked to clean up, deduplicate, or reorganize the vault:

1. Full inventory — search_files(target="files", pattern="*.md") to list every note.
2. Find empties — read_file each file; 0-byte files get deleted. Use terminal with rm for deletion (no dedicated delete tool).
3. Spot duplicates — read every file. Notes covering the same topic with overlapping content are candidates for merge. Two skill catalogs that list the same items in different formats → keep the newer/richer one, delete the other.
4. Merge thin notes — if a standalone note has ≤5 lines of unique content and that content already exists in a larger canonical note, merge the unique bits into the canonical note and delete the thin one.
5. Fix wikilinks — after any deletion, search for [[Deleted Name across all .md files and update to the new canonical target.
6. Use redirect stubs — when a deleted file still has incoming wikilinks you can't or shouldn't rewrite (e.g. thin MOC pages that many notes link to), replace the full content with a 3-5 line redirect note pointing to the canonical file. Include yaml frontmatter with the original name and aliases so Obsidian search/completion still works. This shrinks the file from hundreds of bytes to ~250B while keeping all links intact.
7. Verify — re-run search_files(target="files", pattern="*.md") to confirm the final count and structure.

Pitfalls

• Byte-level dedup misses semantic duplicates. Two files can have different content yet cover the same topic with 80% overlap (e.g. two skill catalogs in different formats, or a user profile spread across multiple files). execute_code with os.walk + hashlib.md5 finds exact duplicates; semantic duplicates require reading and comparing actual content.
• Thin MOC files aren't empty but are noise. A vault with 11 MOC pages each at 300-900B of link-only content creates visual clutter without adding value. Merge them into one consolidated page or redirect them all to a single canonical catalog.
• Archives should be respected. If a vault has a documented archive policy (e.g. AGENTS.md says "do not flatten or delete archive contents"), skip the Archive directories entirely during cleanup.

Batch operations

When creating or editing many notes at once (e.g. generating a set of MOC pages per category), use execute_code to batch write_file / patch calls. This is faster than individual tool calls and keeps the workflow atomic.

When using execute_code for vault work, set vault = "/path/to/vault" once at the top and reference it in every call. Paths with spaces must be handled with string concatenation, not shell expansion.