Link Graph

zetl builds a directed graph where nodes are pages and edges are Wikilinks. The graph powers all link-based queries: forward links, backlinks, multi-hop traversal, shortest path, and orphan detection.

Data model

Node — a Markdown page, identified by its title (filename without .md)
Edge — a wikilink from one page to another, with optional alias, heading, or block reference

The graph is built by the Scanner and cached by the Cache for incremental re-scans.

(given directed-graph)
(given multi-hop-traversal)

Queries

Command	Description
`links`	Forward links from a page, with configurable depth
`backlinks`	Pages linking to a target, with depth traversal
`path`	Shortest link path between any two pages
`export`	Full graph as JSON

These are exposed through Graph Queries. With the --with-conclusions flag, link results are cross-referenced with the Reasoning Engine to show what each linked page contributes to the vault’s logic.

Library

Built on petgraph, a Rust graph data structure library.

See also: Scanner, Graph Queries, Vault Diagnostics

Backlinks

Wikilinksline 30
Wikilinksline 21
Wikilinksline 7
Provenanceline 24
Cacheline 45
Cacheline 7
Scannerline 30
Scannerline 15
Performanceline 63
TUIline 36
Local-first Designline 17
Rust for CLIline 32
Rust for CLIline 17
Vault Diagnosticsline 7
Graph Queriesline 49
Graph Queriesline 31
Graph Queriesline 7
Reason Commandsline 52

Linked Pages

Vault Diagnostics

Vault Diagnostics

zetl check validates the vault and reports issues. It examines both the Link Graph and Spindle Lisp content.

(given dead-link-detection)
(given orphan-detection)
(given spl-diagnostics)

Issue types

Dead links

A wikilink that points to a page that doesn’t exist. For example, [[Plugin System]] in this vault is a dead link — there is no Plugin System.md file.

zetl -d . check --dead-links

Orphan pages

Pages with no incoming links — nothing in the vault references them. These may be forgotten drafts or entry points that need a wikilink from somewhere.

zetl -d . check --orphans

Syntax errors

Malformed Wikilinks like unclosed brackets.

Graph Queries

zetl exposes the Link Graph through several query commands. All output JSON by default — see JSON by Default.

(given forward-links-done)
(given backlinks-done)
(given shortest-path-done)

Commands

`zetl links <page>`

Show all pages that <page> links to. Supports --depth N for multi-hop traversal and --fuzzy for approximate page name matching.

`zetl backlinks <page>`

Show all pages that link to <page>. Same depth and fuzzy options as links.

`zetl path <from> <to>`

Find the shortest chain of Wikilinks connecting two pages. Useful for discovering how ideas relate through intermediate notes.

`zetl export`

Dump the entire Link Graph as JSON — every page and every link.

Scanner

The scanner is zetl’s entry point for understanding a vault. It walks every Markdown file and standalone .spl file, extracting Wikilinks and Spindle Lisp blocks in a single pass.

Wikilink extraction

The scanner recognises all common wikilink forms:

[[Page]] — basic link
[[Page|alias]] — aliased link
[[Page#heading]] — heading anchor
[[Page^block-id]] — block reference
![[Page]] — embed

Extracted links feed into the Link Graph for query and traversal.

SPL extraction

Fenced code blocks tagged ```spl are extracted verbatim, along with their source file and line number. Standalone .spl files anywhere in the vault are also picked up. Both feed into the Reasoning Engine with full Provenance.

(given wikilink-extraction)
(given spl-extraction)

Implementation

Built on pulldown-cmark for Markdown parsing and ignore for .gitignore-aware file walking. The scanner is deliberately read-only — see Local-first Design.

See also: Cache, Link Graph, Reasoning Engine

Reasoning Engine

Reasoning Engine

The reasoning engine takes Spindle Lisp extracted by the Scanner from across the entire vault, merges it into a single theory, and computes conclusions using Defeasible Reasoning. Every conclusion carries full Provenance — you can trace any result back to the exact file and line that contributed to it.

Pipeline

Extract — Scanner finds SPL blocks in Markdown fences and .spl files
Parse — spindle-parser converts SPL text into rule objects
Provenance — source file, line number, and page name are attached to each rule and fact
Combine — all rules and facts are merged into a single theory
Validate — check for undefined labels, duplicate definitions
Reason — spindle-core computes conclusions
Annotate — each conclusion is traced back to its proof sources

(given spindle-core-integrated)
(given four-conclusion-types)

Conclusion types

The engine produces four types of conclusion — see Defeasible Reasoning for details:

Tag	Meaning
`+D`	Definitely provable
`-D`	Definitely not provable
`+d`	Defeasibly provable
`-d`	Defeasibly not provable

Feature gate

The reasoning engine is compiled only when --features reason is enabled — see Feature Gates. Without it, zetl reason prints a clear error rather than failing silently.

See also: Reason Commands, Provenance, Spindle Lisp

Cache

Cache

zetl uses mtiame-based incremental caching for both the Link Graph and the Reasoning Engine’s theory. On subsequent runs, only files modified since the last scan are re-parsed.

How it works

The cache lives in .zetl/ at the vault root:

index.json — serialised link graph
theory.json — serialised reasoning theory and conclusions

Each entry records the file’s last-modified timestamp. When zetl starts, it compares mtimes and only re-scans changed files. Use --no-cache to force a full rebuild.

(given mtime-based-cache)
(given incremental-rebuild)

Design tension

There is an unresolved design tension in how aggressively to cache reasoning results:

; Cache the theory for fast startup
(normally r-cache-theory
  mtime-based-cache
  cache-reasoning-results)

; But recomputing ensures results are always fresh
(normally r-recompute-theory
  incremental-rebuild
  (not cache-reasoning-results))

Both arguments have merit. Try zetl reason conflicts on this vault to see how zetl surfaces this kind of tension. A future Plugin System could let users configure the trade-off.

Safety

Wikilinks

Wikilinks are inline references between pages using [[double bracket]] syntax. They are the primary connective tissue in a zetl vault, forming the edges of the Link Graph.

Syntax

Form	Example	Description
Basic	`[[Cache]]`	Link to a page
Aliased	`[[Cache\|caching layer]]`	Display text differs from target
Heading	`[[Cache#Design tension]]`	Link to a specific heading
Block	`[[Cache^summary]]`	Link to a block ID
Embed	`![[Cache]]`	Embed the target page inline

How zetl uses them

The Scanner extracts wikilinks from every Markdown file. The Link Graph stores them as directed edges, enabling:

Forward link queries (zetl links)
Backlink queries (zetl backlinks)
Shortest path computation (zetl path)
Dead link detection (zetl check)

Cross-referencing with logic

When reasoning is enabled, --with-conclusions annotates link results with the Spindle Lisp conclusions that each linked page contributes. This bridges the Link Graph and the Reasoning Engine.

Compatibility

zetl supports the wikilink conventions used by Obsidian, Logseq, Foam, and Dendron. See Local-first Design for the principle that zetl never modifies your files.