Percolate concepts and relationships

Keep the graph authored, local, and reviewable. wordcell percolate proposes candidates from deterministic evidence; it never changes a note. Backlinks, graph reports, and QMD results are derived views, while Markdown remains the authority.

Locate the vault

• Resolve <vault> to the directory containing its authored or managed index.md front door.
• Read the applicable repository and vault instructions before editing.
• Pass the resolved path to every --root.
• Identify the note or small neighborhood changed by the current task. Prefer a bounded review to a vault-wide cleanup during parallel work.

Inspect candidates

Run percolation on the changed note when possible:

wordcell percolate notes/example --root "$KB_ROOT" --limit 25 --json

Run it without a note only when reviewing the whole vault:

wordcell percolate --root "$KB_ROOT" --min-support 2 --limit 50 --json

Treat each result as a prompt to open the cited notes and read the relevant prose. Candidate kinds may include:

• a recurring tag with no maintained type: concept note;
• notes that share a concept or tag but have no explicit relationship;
• an exact title or alias mentioned without a contextual link;
• a self, reciprocal, malformed, broken, or ambiguous authored relationship.

For missing relationships, support counts independent shared tags or concept neighbors; the evidence array shows the participating notes. The default minimum of two therefore requires two shared signals, not merely both endpoints of one tag match. Other candidate kinds count their natural unit: supporting notes, mention occurrences, or authored hygiene evidence.

For a missing concept, use suggestedId. When collidesWith is non-null, the natural ID is already an ordinary note, so KB chooses an unoccupied *-concept ID. Read the occupied note before deciding whether to create the suggested concept or promote and improve the existing note instead.

Semantic search may help discover evidence, but similarity is never enough to author an edge.

Promote durable concepts

Create a concept only when the idea is likely to be reused and its definition can be stated from the source material:

wordcell note create notes/local-first \
  --root "$KB_ROOT" \
  --title "Local-first" \
  --type concept \
  --tag architecture \
  --body '# Local-first

A concise reviewed definition grounded in the cited notes.'

Write a concise definition and cite or link the notes that establish it. Concepts are ordinary Markdown notes, so they can carry aliases, evidence, context, and their own outbound relationships. Do not create a concept merely to mirror every tag.

After promotion, rerun percolation on the cited non-concept notes. The new concept may support relationships among its neighbors even when a run scoped to the concept itself has no candidate:

wordcell percolate notes/write-path --root "$KB_ROOT" --limit 25 --json

Author typed relationships

Add a relationship from the note that owns the assertion:

wordcell relation add notes/write-path supports notes/durable-agent-memory \
  --root "$KB_ROOT"

Use a specific lower-kebab-case predicate. Targets are exact vault-root note IDs without .md. Ground the assertion in nearby prose or evidence; the frontmatter is an indexable statement, not a substitute for explanation.

List or remove relationships without editing reciprocal notes:

wordcell relation list notes/write-path --root "$KB_ROOT" --json
wordcell relation remove notes/write-path supports notes/durable-agent-memory \
  --root "$KB_ROOT"

Never write inverse edges, generated backlinks, inferred transitive relationships, or semantic-search scores into Markdown. Those are derived views.

Query before concluding

Use exact structure to verify that the promoted graph says what the prose says:

wordcell links notes/write-path --root "$KB_ROOT" --direction both --depth 2 --json
wordcell relation list notes/write-path --root "$KB_ROOT" --json
wordcell graph --root "$KB_ROOT" --json

Prefer the note-scoped commands first. Use the whole-vault graph only when the question spans several neighborhoods, and confirm returned IDs against their Markdown notes before reporting a conclusion.

Finish under the vault's catalog mode

When working alone or integrating several lanes:

wordcell refresh --root "$KB_ROOT"
wordcell check --root "$KB_ROOT"

When several agents are editing different notes in a managed-catalog vault, each lane should validate authored structure and local attachments without rewriting the shared catalog:

wordcell check --root "$KB_ROOT" --no-catalog

The integrating agent runs one final managed refresh and normal check. In an authored-catalog vault, refresh and check leave the front door untouched, while wordcell catalog --root "$KB_ROOT" renders an exhaustive disposable inventory. Resolve same-note Git conflicts from the prose and evidence; do not accept one side's frontmatter mechanically.