Wiki

A wiki is a structured, indexed knowledge base organized as a folder tree with _index.md files. Each folder has an index that links to its children (subfolders and pages), and a content section below a *** delimiter for user-authored notes.

Initialize a wiki in the current project and configure integrations:

• wiki init — scaffold a new wiki with a root index
• wiki config — install Obsidian plugins and the git merge driver
• wiki trust — authorize a wiki to run its .wiki/wiki.py hook

Maintain indexes as files are added and removed:

• wiki lint — validate structure and flag issues
• wiki update — sync index links with the filesystem

Browse structure, search across content, and read entries:

• wiki map — print an indented tree overview
• wiki search — search content with regex
• wiki read — read a named entry

Usage

Install the CLI from PyPI if it is not already on your PATH:

pipx install plasma-wiki

(pip install or uv tool install work too.)

Then run commands directly:

wiki <command> ...

Run wiki --help for a list of commands, and wiki <command> --help for full option descriptions.

Working at scale

A wiki is many small, independent pages, so wiki work parallelizes well and is often too large for one context. Default to sub-agents and dynamic workflows rather than authoring or auditing page by page yourself:

• Fan out sub-agents. When seeding or expanding a wiki, give each independent page — or each source to research and digest — to its own sub-agent, then run wiki update once to stitch the new pages into the indexes. Update adds and repairs index link rows and frontmatter only — it never linkifies mentions in page prose, so author [[...]] cross-links by hand.
• Drive sweeps with a dynamic workflow. When auditing, relinking, or restructuring an existing wiki, pipeline its pages through a workflow so each is read, revised, and verified on its own — slow pages never block fast ones.

Conventions

• .wiki/ is the tool's namespace. Every root carries a .wiki/ directory holding settings.json — the file that declares the wiki root; wiki init writes it and wiki update restores a missing one — plus the derived word-counts cache and the staged Obsidian config. Never author content there; the walk skips dot-directories by construction.
• Exclusions are configurable. Beyond the built-ins (dot-paths, symlinks, _index.md), gitignore-style globs in exclude.patterns in .wiki/settings.json exclude whole subtrees from indexing — never walked, scaffolded, or linted, though wiki read still serves them.
• Name validation is configurable. By default the wiki rejects only structural characters (/, \, *, [, ], |, #), a leading dot, and the reserved _index stem — spaces, dashes, and unicode all pass. Stricter rules (e.g. ASCII identifiers) are opt-in per wiki via naming.validate in .wiki/settings.json (seed it at creation with wiki init --settings); wiki init and wiki lint enforce whatever policy is set.
• Timestamps are tool-owned and configurable. wiki update writes both stamps when a file gains frontmatter, keeps created: from then on, and rewrites updated: on every actual write — never hand-edit them; an edit goes undetected unless the value stops parsing under the configured format, which wiki lint fails. created/updated default to UTC in %Y-%m-%dT%H:%M:%SZ; set timestamp.timezone (an IANA name) and timestamp.format (a strftime string) in .wiki/settings.json to change them — use %z rather than a literal Z for a non-UTC zone.
• Names are path-derived; titles are authored. wiki update sets each page's name and H1 heading to the path-joined name (e.g. core/design) so names stay consistent with the tree structure — to rename an entry, move its file rather than editing name:. Any index or page may carry an optional authored title: frontmatter field, which wins its H1 (wiki update keeps the line directly under name:, and adding frontmatter to a bare page seeds title: from its authored H1); without one, a hand-edited heading is still rewritten to name. Unset a title by deleting the line or setting title: null — update removes it, and lowercase null is the only reset spelling (~/Null/NULL render literally as the heading). Keep titles on a single line, quote a title containing : , and prefer plain text. wiki search --field title matches only authored titles — an unset entry has no line to match. Setting titles.required to true in .wiki/settings.json demands a title everywhere: update seeds a title: null placeholder on every index and page missing one, and lint fails each placeholder until a value is authored.
• Categories are authored and optional. An index or page may carry a category: frontmatter field; wiki update copies it into the parent index's link label as a [category] name prefix, and wiki map --category filters by it. Fresh frontmatter carries no category: line — unset one by deleting the line or setting category: null (update removes the line; as with titles, lowercase null is the only reset spelling). Keep categories on a single line.
• Frontmatter order is tool-enforced. wiki update keeps every block in canonical order — name, title, desc, category, tags, sources, created, updated — moving each field (with its block-scalar body) verbatim into its slot. Custom keys are allowed: they keep their relative order below the known fields, above the timestamps.
• Wikilinks stay inside the wiki. A wikilink ([[...]]) must target another page in the same wiki. Files outside the wiki (source files, configs, another wiki's pages) can be referenced by name or in backticks, but never linked.
• Stale wikilinks are soft notes. A [[...]] in index or page prose whose target no longer exists draws a stderr note from wiki lint without failing the run. Broken links in the generated index link block — the rows wiki update maintains — stay hard issues (--prune removes them), as does a prose wikilink naming a folder rather than the folder's index page: link [[folder/_index]], never [[folder]].
• Descriptions end in a period. wiki lint fails a desc (or an authored link description) that lacks a trailing period; the seeded ... placeholder only draws a soft note. Author the desc in the child page's frontmatter — wiki update copies it onto the parent index's link line. A desc containing : must be YAML-quoted; surrounding quotes are stripped when the value is read. Never hand-wrap a desc mid-word or onto a list-marker start — let the block scalar carry the breaks; lint fails the wrap artifacts (a hyphen dangle, a phantom list item).
• Fill in auto-created index descs. wiki update creates a missing _index.md for every new directory with a desc: ... placeholder and announces the batch in its condensed summary (Created N new indexes (fill in their descs); run with --full for the per-path New index: lines). Fill in the desc right after the update — lint soft-notes the placeholder until you do.
• Bare pages are adopted loudly. A page with no frontmatter gains it on the next wiki update — with title: seeded from its authored H1, while a page with no H1 gains the path-joined heading in its body, never a seeded title — and each adoption is announced (Adopted N bare pages (frontmatter added) in the condensed summary; --full prints the per-page lines). Until then wiki lint names the page as a hard issue (Bare page (no frontmatter); update will adopt it) alongside the adoption diff.
• Suppress lint locally with a no-lint region. A page that must display otherwise-flagged content (sample conflict markers, stale link examples) wraps those lines in <!-- start: no-lint --> ... <!-- end: no-lint -->, which silences the positional rules — hard issues and soft notes alike — for just that span. Regions never affect file-level checks, and a dangling or nested marker is itself a hard lint issue.
• Give markdown formatters the wiki plugin. The *** delimiter and [[wikilinks]] are load-bearing syntax; mdformat/prettier-style hooks rewrite *** to --- and escape the brackets, demoting the generated link block to plain text. wiki update repairs a mangled index and wiki lint names the damage signatures (escaped wikilinks, a thematic break standing where *** belongs), but don't rely on the repair: for mdformat add the mdformat-wiki plugin (under pre-commit, additional_dependencies: [mdformat-wiki] on the hook, dropping a coexisting mdformat-frontmatter — both register a frontmatter renderer and whichever is discovered first wins), which makes wiki faces round-trip byte-identically; for formatters with no plugin lane (e.g. prettier) exclude the wiki root instead (wiki/ in .prettierignore).
• The git merge driver resolves only the generated region. For _index.md files it takes ours for the regenerated parts above *** (the link block plus the name/updated keys wiki update regenerates) and three-way merges everything authored — the remaining frontmatter fields (title/desc/created/category/tags/ sources) and the user content below *** — which can still conflict for hand-resolution. A side missing its *** entirely (formatter damage) can't be split into regions, so it conflicts whole-file with a hint comment naming the repair — restore the *** on that branch (wiki update does it), then redo the merge. Run wiki update after a merge to regenerate the link rows from the filesystem — the H1 rides the taken-ours region, so a merged-in title: shows in its H1 only after that update. init/config register the driver in local git config and write the **/_index.md glob to .gitattributes in the working tree only — you stage and commit it yourself, and each clone runs wiki config once to register the driver.
• Leave new-directory index bodies empty during concurrent work. When sibling branches both create the same new directory, its two _index.mds merge add/add with no common ancestor: the generated region resolves automatically — including the seeded created stamps, which are wiki update churn on both sides — but body prose authored below *** on both sides conflicts for hand-union (empty or identical bodies merge clean). Concurrent cohorts should leave a new directory's index body empty until after the merge wave, then author it once. The merge driver plants a one-line HTML-comment hint above such add/add conflict markers naming this convention — delete it as you resolve.
• A .wiki/wiki.py hook needs explicit trust. A wiki may ship a .wiki/wiki.py (a custom Wiki subclass) that runs code with the user's privileges, so wiki refuses to load an untrusted hook — every command that resolves the wiki fails, naming the hook and pointing at wiki trust. This is a security decision for the human: surface the error and let the user run wiki trust for a wiki they have vetted, rather than running it yourself or working around the refusal. A hookless wiki needs no trust; trust is recorded per resolved root in ~/.wiki/settings.json (WIKI_CONFIG_DIR overrides the config home).