Why layer: CLI and read-only MCP

The Why layer indexes local Claude Code, Codex, DeepSeek Harness, and ThoughtDAG canvas conversations together. Start with a file, an exact phrase, a URL, or an arXiv paper id; the result points back to the matching turn.

Install

Try one query without installing:

npx thoughtdag why src/lib/api.ts

For regular use, install the command globally and build the local index:

npm install -g thoughtdag
thoughtdag index

Connect the read-only MCP server

From the project where you want to use it:

thoughtdag setup mcp

This registers ThoughtDAG in the current project's .mcp.json for Claude Code and in ~/.codex/config.toml for Codex. Queries remain scoped to the current workspace. The MCP server can search and recall; it cannot edit a canvas or a source session.

Optionally add project rules

thoughtdag setup rules
thoughtdag setup rules --remove

The first command adds a marked block to this project's CLAUDE.md and AGENTS.md, asking agents to check relevant history before editing a file. The second removes only that block. Nothing is added to a global instruction file.

CLI reference

For native Harness queries and their release status, see the DeepSeek Harness plugin. Native why_find and why_recall correspond to MCP find and recall_turn below.

Command	Purpose
thoughtdag index [--full] [--canvas <dir>]	Build or refresh the index; optionally remember a canvas-backup directory
thoughtdag why <path> [--include-read] [--all] [--limit N] [--json]	Show turns that touched a file, URL, or paper
thoughtdag why --check <path> [--fresh] [--json]	Cheap check for whether an artifact has history
thoughtdag find "<phrase>" [--in q|a|m] [--limit N] [--json]	Exact, case-insensitive search across questions, answers, or materials
thoughtdag recall <session> <n>	Print one turn in full
thoughtdag status	Show index size and evidence coverage
thoughtdag purge [--cache]	Delete all derived data, or only rebuildable caches
thoughtdag events <session-file> [--touches]	Project one source file into canonical events
thoughtdag mcp	Serve the four read-only tools over stdio MCP
thoughtdag setup [mcp | rules [--remove]]	Inspect or change project integration

<path> may be an absolute path, a path relative to the current workspace, a URL, or arxiv:<id>.

MCP tool dictionary

Tool	Arguments	Returns
why_check	path	One-line history yes/no check
why_file	path, optional include_read, limit	Matching turns and observed file changes
find	phrase, optional in, limit	Exact matches in questions (q), answers (a), materials (m), or all three
recall_turn	session, turn	Full question, answer, and tool trail for one turn

Output dictionary

Marker	Meaning
Q	The user's question, verbatim excerpt
A	The agent's answer, verbatim excerpt
M	Text attached to a ThoughtDAG canvas node
Δ	Observed edit or write from a tool call
≈	Candidate explanation inferred from the answer; not a verified fact
↗	Pointer back to the source turn or canvas node

Examples

Find the conversations that changed a file

$ thoughtdag why src/lib/api.ts
why src/lib/api.ts · 12 turns in 6 sessions
claude-code  ✏️ edit  Q: Can the API detect vision support?
             Δ storedProviders → storedProviders, storedVision…

Add --include-read when read-only touches also matter. Use --all to remove the default result cap.

Find where a concept appeared

$ thoughtdag find "context.committed" --in q
find "context.committed" · 21 turns in 12 sessions
claude-code  Q: …add context.committed to the event contract…
codex        Q: …context.committed is already half implemented…

Use --in a for answers and --in m for canvas materials.

Find a paper or webpage

thoughtdag why arxiv:2606.26733
thoughtdag why https://example.org/paper
thoughtdag find "arxiv" --in m

Open one matching turn in full

Copy the session id and turn number shown by why or find:

thoughtdag recall <session-id> <turn-number>

If the desktop app is installed, the ↗ link opens the matching turn or canvas node.

For the visual session browser and editable context graph, continue with Session Atlas.