agent-doc

Alpha Software — actively developed, APIs and frontmatter format may change between versions. Feedback welcome via GitHub issues.

Interactive document sessions with AI agents.

Edit a markdown document. Press a hotkey. The tool diffs your changes, sends them to an AI agent, and writes the response back into the document. The document is the UI.

Why

Terminal prompts are ephemeral. You type, the agent responds, the context scrolls away. Documents are persistent — you can reorganize, delete noise, annotate inline, and curate the conversation as a living artifact. The agent sees your edits as diffs, so every change carries intent.

Install

cargo install --path .

Quick Start

agent-doc init session.md "Topic Name"    # scaffold a session doc
agent-doc run session.md                  # diff, send, append response
agent-doc diff session.md                 # preview what would be sent
agent-doc reset session.md                # clear session + snapshot
agent-doc clean session.md                # squash session git history
agent-doc route session.md               # route to tmux pane (or auto-start)
agent-doc start session.md               # start Claude in current tmux pane
agent-doc claim session.md [--window W]  # claim file for a tmux pane
agent-doc focus session.md               # focus tmux pane for a session
agent-doc layout a.md b.md --split h [--window W]  # arrange panes (window-scoped)
agent-doc outline session.md             # section structure + token counts
agent-doc outline session.md --json      # JSON output for tooling
agent-doc patch dashboard.md status "new content"  # update a component
agent-doc watch                          # auto-submit on file change
agent-doc parallel session.md --task "task 1" --task "task 2"  # parallel fan-out
agent-doc resync                         # validate sessions, prune dead panes
agent-doc resync --fix                   # also fix wrong-session/wrong-process panes
agent-doc commit session.md              # git add + commit with timestamp
agent-doc prompt session.md              # detect permission prompts → JSON
agent-doc skill install                  # install Claude Code skill definition
agent-doc skill check                    # check if skill is up to date
agent-doc upgrade                        # upgrade to latest version
agent-doc plugin install <editor>        # install editor plugin (jetbrains|vscode)
agent-doc plugin update <editor>         # update editor plugin to latest
agent-doc plugin list                    # list available editor plugins

Document Format

---
agent_doc_session: 05304d74-90f1-46a1-8a79-55736341b193
agent: claude
---

# Session: Topic Name

## User

Your question or instruction here.

## Assistant

(agent writes here)

## User

Follow-up. You can also annotate inline:

> What about edge cases?

Frontmatter fields

Field	Required	Default	Description
agent_doc_session	no	(generated on first run)	Document UUID for tmux pane routing (legacy: session)
agent_doc_format	no	template	Document format: inline (canonical) or template. append accepted as backward-compat alias for inline.
agent_doc_write	no	crdt	Write strategy: merge or crdt
agent_doc_mode	no	—	Deprecated. Use agent_doc_format + agent_doc_write instead
resume	no	(none)	Claude conversation ID for --resume
agent	no	claude	Agent backend to use
model	no	(agent default)	Model override
branch	no	(none)	Git branch for session commits
claude_args	no	(none)	Additional CLI args for claude process (space-separated)

Two interaction modes

Append mode: Structured ## User / ## Assistant blocks.

Inline mode: Annotations anywhere — blockquotes, edits to previous responses. The diff captures what changed; the agent addresses inline edits alongside new ## User content.

Both work simultaneously because the run sends a diff, not a parsed structure.

Run Flow

┌──────────┐  hotkey ┌────────────┐  diff + prompt  ┌───────┐
│  Editor  │ ──────> │ agent-doc  │ ──────────────> │ Agent │
│          │         │            │ <────────────── │  API  │
│  reload  │ <────── │ write+snap │                 └───────┘
└──────────┘         │ git commit │
                     └────────────┘

1. Read document, load snapshot (last-known state)
2. Compute diff — if empty, exit (double-run guard)
3. Send diff + full document to agent, resuming session
4. Append response as ## Assistant block
5. Save snapshot, git commit

Session continuity

• Empty agent_doc_session: — forks from the most recent agent session in the directory (inherits context)
• agent_doc_session: <uuid> — resumes that specific session
• Delete agent_doc_session: value — next run starts fresh

History rewriting

Delete anything from the document. On next run, the diff shows deletions and the agent sees the cleaned-up doc as ground truth.

Components

Components are bounded, named regions in a document that can be updated independently:

<!-- agent:status patch=replace -->
| Service | State   |
|---------|---------|
| api     | healthy |
<!-- /agent:status -->

Inline attributes on the tag override components.toml and built-in defaults. Precedence: inline attr > components.toml > built-in defaults.

Component marker detection uses pulldown-cmark for CommonMark-compliant parsing: tags inside inline code spans or fenced code blocks are ignored and never treated as component boundaries.

Standard component names

Component	Default patch	Description
exchange	append	Conversation history — each cycle appends
findings	append	Accumulated research data — grows over time
status	replace	Current state — updated at milestones
pending	replace	Task queue — auto-cleaned each cycle
output	replace	Latest agent response only
input	replace	User prompt area
(custom)	replace	All other components default to replace

Update a component:

agent-doc patch dashboard.md status "| api | healthy |"
echo "deploy complete" | agent-doc patch dashboard.md log

Component config

Configure modes and hooks in .agent-doc/components.toml:

[log]
mode = "append"        # append | replace (default) | prepend
timestamp = true       # auto-prefix with ISO timestamp
max_entries = 100      # trim old entries

[status]
pre_patch = "scripts/validate.sh"   # transform content (stdin → stdout)
post_patch = "scripts/notify.sh"    # fire-and-forget after write

Dashboard-as-document

A dashboard is a markdown document with agent-maintained components. External scripts update components via agent-doc patch, and the watch daemon can auto-trigger agent responses:

# Start watching for changes
agent-doc watch

# Update from CI scripts
agent-doc patch monitor.md builds "$(./format-builds.sh)"
agent-doc patch monitor.md log "Build #${BUILD_ID}: ${STATUS}"

See Components guide and Dashboard tutorial for full documentation.

Git Integration

Each run auto-commits the document for inline diff highlighting in your editor.

Flag	Behavior
-b	Auto-create branch agent-doc/<filename> on first run
(none)	Commit to current branch
--no-git	Skip git entirely

Cleanup: agent-doc clean <file> squashes all session commits into one.

Configuration

claude_args

Pass additional CLI arguments to the claude process spawned by agent-doc start. Three sources, highest precedence first:

1. Document frontmatter (per-document):

---
agent_doc_session: 05304d74-...
claude_args: "--dangerously-skip-permissions"
---

2. Global config (~/.config/agent-doc/config.toml):

claude_args = "--dangerously-skip-permissions"

3. Environment variable:

export AGENT_DOC_CLAUDE_ARGS="--dangerously-skip-permissions"

Args are split on whitespace and prepended to the claude command before other flags.

Agent Backends

Agent-agnostic core. Only the "send prompt, get response" step varies.

# ~/.config/agent-doc/config.toml

[agents.claude]
command = "claude"
args = ["-p", "--output-format", "json"]
result_path = ".result"
session_path = ".session_id"

[agents.codex]
command = "codex"
args = ["--prompt"]
result_path = ".output"
session_path = ".id"

default_agent = "claude"

Override per-document via agent: in frontmatter, or per-invocation via --agent.

Tmux Session Routing

Route documents to persistent Claude sessions via tmux. Pane management is powered by tmux-router.

agent-doc route plan.md    # send to existing pane, or auto-start one
agent-doc sync --col a.md,b.md --col c.md --focus a.md  # 2D layout sync

How it works:

1. Each document gets an agent_doc_session UUID in frontmatter (auto-generated if missing)
2. agent-doc maps UUIDs to file paths, then delegates to tmux-router for pane routing
3. route checks if the pane is alive — if so, sends the command (with Enter retry verification) and focuses the pane
4. If the pane is dead (previously registered), route lazy-claims to an active pane in the claude tmux session, syncs the layout, then sends the command
5. New/unregistered files skip lazy-claim and go directly to auto-start, so each file gets its own Claude session
6. If no active pane is available, auto-starts a new Claude session in tmux: first tries split-window in an existing window that has a registered agent-doc pane (avoids creating throwaway windows), falls back to creating a new window if no registered panes exist (30s startup timeout with ❯ prompt detection)
7. sync auto-starts Claude sessions for files with session UUIDs but no alive panes before arranging the layout

Parallel — Fan-Out

Decompose a complex task into independent subtasks, each running in its own git worktree with a separate Claude session.

CLI

agent-doc parallel plan.md \
  --task "Implement auth middleware in src/auth.rs" \
  --task "Write integration tests for auth" \
  --task "Update API docs for auth endpoints" \
  --model opus \
  --timeout 600

Flag	Description
--task "..."	Subtask description (repeatable, at least 1)
--model <model>	Model override for subtask agents
--timeout <secs>	Per-task timeout (default: 600)
--no-git	Skip git commits in worktrees
--dry-run	Print plan without executing

How it works

1. Creates a git worktree per task (.agent-doc/worktrees/<session>-<n>)
2. Writes task prompt to each worktree
3. Spawns claude -p in stashed tmux panes (one per worktree)
4. Polls for completion every 2 seconds
5. Collects results: agent JSON output + git diff HEAD per worktree
6. Prints formatted markdown with collapsible diffs

From a document session

In a template-mode document, write a deep: directive in the exchange:

deep:
- Implement auth middleware
- Write integration tests
- Update API docs

The SKILL.md skill parses the deep: prefix, extracts bullet tasks, and calls agent-doc parallel --task "..." --task "...". Results are written back to the exchange.

Resync

Validate sessions.json against live tmux state and fix inconsistencies.

agent-doc resync          # dry-run: prune dead panes, report issues
agent-doc resync --fix    # also fix detected issues

Dry-run (no --fix): Removes entries whose tmux panes no longer exist, purges idle stash windows (30s grace period), logs orphaned claude/stash windows, and reports wrong-session, wrong-process, or wrong-window panes without changing them.

With --fix:

• Wrong-session panes (pane is in a different tmux session than the document's tmux_session frontmatter) — kills the pane and deregisters it. The next route auto-starts in the correct session.
• Wrong-process panes (pane is running a non-agent-doc process, e.g. corky watch) — deregisters the entry but leaves the foreign process alive.
• Wrong-window panes (pane is in a separate non-stash window from the majority of panes in the same tmux session) — moves the pane into the stash window via stash_pane. The next sync or layout will rejoin it into the correct window.

Stash windows: When split-window fails during auto-start (e.g. minimum pane size constraint), the new pane is created in a fresh window and immediately moved to the stash window so no extra visible windows appear. Stash windows are named stash; if tmux auto-deduplicates the name they become stash-2, stash-3, etc. — all such names are recognized and eligible for purging.

Process allowlist: agent-doc, claude, node are valid agent processes. Idle shells (zsh, bash, sh, fish) are also allowed (a shell means the agent process hasn't started yet or has exited).

Automatic pruning: resync::prune() runs automatically before route, sync, and claim operations — you only need to run agent-doc resync explicitly for diagnostics or --fix.

IPC-First Writes

Since v0.17.5, all write paths (run, stream, write) try IPC to the IDE plugin when .agent-doc/patches/ exists (plugin installed) and --force-disk is not set. agent-doc writes a JSON patch to .agent-doc/patches/ instead of modifying the file directly. The plugin applies the change via Document API, preserving cursor position, undo history, and avoiding "externally modified" dialogs. On IPC timeout (2s), exits with code 75 (EX_TEMPFAIL) instead of falling back to disk write. Use agent-doc write --force-disk to bypass IPC and write directly to disk.

Editor Integration

JetBrains

External Tool: Program=agent-doc, Args=run $FilePath$, Working dir=$ProjectFileDir$, Output paths=$FilePath$. Assign keyboard shortcut.

VS Code

Task: "command": "agent-doc run ${file}". Bind to keybinding.

Vim/Neovim

nnoremap <leader>as :!agent-doc run %<CR>:e<CR>

CLI Reference

agent-doc run <file> [-b] [--agent <name>] [--model <model>] [--dry-run] [--no-git]
agent-doc init <file> [title] [--agent <name>]
agent-doc diff <file>
agent-doc reset <file>
agent-doc clean <file>
agent-doc route <file>              # route to existing tmux pane or auto-start
agent-doc start <file>              # start Claude session in current tmux pane
agent-doc claim <file> [--window W] [--pane P]  # claim file for a tmux pane
agent-doc focus <file> [--pane P]              # focus tmux pane for a session
agent-doc layout <files> --split h [--window W] # arrange panes (window-scoped)
agent-doc outline <file> [--json]    # section structure + token counts
agent-doc parallel <file> --task "..." [--model M] [--timeout S] [--dry-run]  # parallel fan-out
agent-doc resync                    # validate sessions, prune dead panes, report issues
agent-doc resync --fix              # also kill wrong-session panes, deregister wrong-process panes
agent-doc prompt <file> [--all]     # detect permission prompts → JSON
agent-doc prompt --answer N <file>  # answer prompt option N
agent-doc commit <file>             # selective commit (snapshot only, user edits stay uncommitted)
agent-doc terminal <file> [--session S]  # launch terminal with tmux for editor plugins
agent-doc skill install             # install Claude Code skill definition
agent-doc skill check               # check if installed skill is up to date
agent-doc patch <file> <component> [content]  # update component (stdin if no content)
agent-doc watch [--stop] [--status]          # watch daemon (debounce + reactive mode for stream docs)
agent-doc write <file> --force-disk  # bypass IPC, write directly to disk
agent-doc history <file>            # list exchange versions from git
agent-doc history <file> --restore <commit>  # prepend old exchange content
agent-doc audit-docs                # audit instruction files for staleness
agent-doc upgrade                   # upgrade to latest version
agent-doc plugin install <editor>   # install editor plugin (jetbrains|vscode)
agent-doc plugin update <editor>    # update editor plugin to latest
agent-doc plugin list               # list available editor plugins

Domain Ontology

agent-doc extends the existence kernel vocabulary (defined in ~/.claude/philosophy/src/) with domain-specific terms for interactive document sessions.

Term	Derives From	Description
Session	project + story	A bounded interaction with temporal arc; the unit of agent-doc work
Document	entity + context	A markdown file that holds conversational state between user and agent
Pane	focus + scope	A tmux viewport — finite attention applied to a single document
Claim	scope + entity	Binding a document to a pane; scoping focus to a specific file
Route	context + resolution	Resolving which pane handles a document; context-aware dispatch
Sync	pattern + system	Aligning tmux pane layout to editor split state; maintaining coherence
Watch	consciousness + evolution	Detecting file changes and triggering agent responses; event-driven
Dashboard	system + focus	A document used as a live system view with agent-maintained sections
Component	scope + abstraction	Bounded, named, re-renderable region in a document (<!-- agent:name -->...<!-- /agent:name -->). Configurable mode (replace/append/prepend) and shell hooks.
Registry	system + perspective	Persistent mapping of documents to panes; the routing state
Snapshot	entity + story	Point-in-time capture of document content for diff computation
Project	system + scope	The bounded working context; identified by .agent-doc/ at its root. Contains documents, registry, snapshots, daemon. tmux-router is project-agnostic.
Overlay	context + resolution	Domain-specific terms extending the base kernel vocabulary

License

MIT