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Creates a new article in the library — a paper someone else wrote.

Records a design decision on a study — what was chosen, what was not, and WHY.

Creates a free-form journal entry in the active project — the right home for an observation, reflection, or cross-cutting thought that is not tied to a specific paper.

Adds a new excerpt (quote + optional comment) to an existing article.

Adds a hypothesis to a study.

Appends text to an existing article's notes field.

Creates a new top-level project — an isolated container with its own themes, questions, library, and journal.

Adds a new research question to an existing theme.

Attaches a user source to a research question — a reference you want kept next to the question that is not (yet) an article in the library: a book, a talk, a URL, a citation from elsewhere.

Creates a study — original research being designed, as opposed to a paper someone else wrote.

Creates a new research theme.

Permanently removes an article from the library by ID.

Permanently removes a decision.

Permanently removes a journal entry by ID.

Removes a specific excerpt from an article by excerpt ID.

Permanently removes a hypothesis.

Soft-deletes a project, matching the app: it disappears from every read but keeps its whole subtree.

Permanently removes a research question and everything hanging off it: its notes, its user sources, its status and starred state.

Permanently removes a note from a research question by note ID.

Permanently removes a user source from a research question by source ID.

Permanently removes a study AND every hypothesis and decision on it.

Deletes a research theme.

Returns full details of a single article by ID, including all excerpts, notes, linked questions, AI summary, and metadata.

Returns journal entries from the active project, newest first.

The full revision history of one hypothesis, oldest to newest.

Returns all saved articles with title, authors, year, tags, status, source, and excerpt count.

Every decision still open — the "what have I not settled yet" list.

Returns all research questions across all themes, with their status, starred state, notes, user sources, and search phrases.

Lists every study in the active project with counts of active hypotheses and open decisions.

Full detail for one study: design prose, every hypothesis and decision (superseded ones included, each carrying the id of what replaced it), and linked questions with their text.

Returns all research themes with their descriptions and which question IDs belong to each.

Links or unlinks an article to a research question by updating the article's linkedQuestions array.

Links or unlinks two research questions as related.

Links or unlinks a study and a research question.

Returns every top-level project with its icon, color, description, and content counts, and marks which one is currently active.

Restores a soft-deleted project with everything it held, and makes it the active project, matching the app.

Restores a soft-deleted theme in the active project, matching Recently deleted in Manage Themes.

Full-text search across the active project: research questions, articles, journal entries, and studies.

Changes which project every other journal_* tool reads and writes.

Reverses a decision in ONE call: records the new decision, marks the old one superseded, and points it at the replacement.

Replaces a hypothesis with a revised version in ONE call: creates the new hypothesis carrying the old one's label and question forward, marks the old one superseded, and points it at the new one.

Updates fields on an existing article.

Edits a decision in place — typically to settle an open one by adding the rationale and setting status='settled'.

Updates an existing journal entry.

Edits a hypothesis in place.

Renames a project or changes its description, icon or color.

Updates a research question.

Replaces the content of an existing note on a research question.

Updates a study.

Sets the tags array on an existing article, replacing whatever tags are currently there.

Renames a research theme or changes its description, color, or icon.

Capture a thought directly from a chat conversation, skipping the app entirely (captureMode: chat).

Soft-delete an entry (starts the 30-day undo window, not instant-gone).

Full entry: transcript, audio ref, timestamp, capture mode.

Untriaged count and keep/discard/promote breakdown.

Mark an entry kept.

Paginated, triaged entries, newest first — the same three views the app's Archive screen offers: kept (default), promoted (sent to another app), or discarded (still inside their 30-day undo window).

Paginated, untriaged entries, newest first.

Flag an entry as sent elsewhere and record the destination.

Retry a voice memo whose transcription timed out (transcriptionStatus: timed_out).

Move a kept, promoted or discarded entry back to the untriaged inbox, clearing its destination and triage time.

Restore an edited entry's transcript to the text as originally captured.

Full-text search across entries by transcript content.

Restore a discarded entry to the status it was discarded from — untriaged if it was discarded during triage, kept if it was deleted from the archive.

Correct an entry's transcript (e.g. a misheard word).

Connect two existing nodes with a directed, typed edge.

Remove an edge between two nodes.

BFS traversal from a starting node outward to `depth` hops.

Run a BFS traversal and return the result as a Mermaid `graph LR` diagram string.

Soft-delete a node.

Create a new node in the Vertexism knowledge graph.

Fetch a single node plus all its edges (both directions).

Full-text search across node names and descriptions.

Update the name, description, or tags on an existing node.

Returns all nodes with no edges, sorted by days orphaned (most neglected first).