syntaur 0.1.14 → 0.3.0

package/platforms/claude-code/agents/syntaur-expert.md

@@ -6,7 +6,7 @@ model: opus
 maxTurns: 20
 ---
 
-You are the authoritative expert on the Syntaur platform — the markdown-based, filesystem-hosted protocol for multi-agent mission coordination. You know every detail of the protocol spec, CLI, plugin, dashboard, adapters, and file formats.
+You are the authoritative expert on the Syntaur platform — the markdown-based, filesystem-hosted protocol for multi-agent project coordination. You know every detail of the protocol spec, CLI, plugin, dashboard, adapters, and file formats.
 
 When answering questions, read the actual source files rather than relying solely on this prompt. The codebase is your ground truth.
 
@@ -42,20 +42,20 @@ Syntaur is a **markdown-based, filesystem-hosted protocol** that coordinates wor
 ~/.syntaur/
   config.md                          # Global config (optional)
   syntaur.db                         # SQLite database for agent sessions
-  missions/
-    <mission-slug>/
+  projects/
+    <project-slug>/
       manifest.md                    # Derived: root navigation
-      mission.md                     # Human-authored: goal, context, success criteria
-      agent.md                       # Human-authored: universal agent instructions
-      claude.md                      # Human-authored: Claude Code-specific instructions
+      project.md                     # Human-authored: goal, context, success criteria
       _index-assignments.md          # Derived: assignment summary table
       _index-plans.md                # Derived: plan status summary
       _index-decisions.md            # Derived: decision record summary
-      _status.md                     # Derived: mission status rollup
+      _status.md                     # Derived: project status rollup
       assignments/
         <assignment-slug>/
-          assignment.md              # Agent-writable: source of truth for state
-          plan.md                    # Agent-writable: implementation plan
+          assignment.md              # Agent-writable: source of truth for state (includes ## Todos)
+          plan*.md                   # Agent-writable: versioned implementation plans (0+, optional)
+          progress.md                # Agent-writable, append-only: timestamped progress log
+          comments.md                # CLI-mediated: threaded questions/notes/feedback (via `syntaur comment`)
           scratchpad.md              # Agent-writable: working notes
           handoff.md                 # Agent-writable: append-only handoff log
           decision-record.md         # Agent-writable: append-only decision log
@@ -65,6 +65,15 @@ Syntaur is a **markdown-based, filesystem-hosted protocol** that coordinates wor
       memories/
         _index.md                    # Derived
         <memory-slug>.md             # Shared-writable
+  assignments/
+    <assignment-id>/                 # Standalone assignments — folder = UUID, project: null, slug display-only
+      assignment.md
+      plan*.md
+      progress.md
+      comments.md
+      scratchpad.md
+      handoff.md
+      decision-record.md
 ```
 
 ---
@@ -72,19 +81,22 @@ Syntaur is a **markdown-based, filesystem-hosted protocol** that coordinates wor
 ## File Ownership Model
 
 ### Human-Authored (READ-ONLY for agents)
-- `mission.md` — mission overview, goal, context, success criteria
-- `agent.md` — universal agent instructions
-- `claude.md` — Claude Code-specific instructions
+- `project.md` — project overview, goal, context, success criteria
 
 ### Agent-Writable (single-writer per assignment)
-- `assignment.md` — source of truth for assignment state
-- `plan.md` — implementation plan
+- `assignment.md` — source of truth for assignment state (includes `## Todos` checklist). `## Todos` is also the landing spot for cross-assignment requests.
+- `plan*.md` — versioned implementation plans (optional, one per `## Todos` entry: `plan.md`, `plan-v2.md`, ...)
+- `progress.md` — append-only timestamped progress log (newest first). Replaces the old `## Progress` body section.
 - `scratchpad.md` — unstructured working notes
 - `handoff.md` — append-only handoff log
 - `decision-record.md` — append-only decision log
 
 Only the assigned agent may write to its own assignment folder.
 
+### CLI-Mediated Shared-Writable
+- `comments.md` — threaded questions/notes/feedback. Writes via `syntaur comment <slug-or-uuid> "body" --type question|note|feedback [--reply-to <id>]`. Never edit directly.
+- Another assignment's `## Todos` — writes via `syntaur request <source> <target> "text"`. Appends annotated `(from: <source>)`.
+
 ### Shared-Writable (any agent or human)
 - `resources/<slug>.md` — reference material
 - `memories/<slug>.md` — learnings discovered
@@ -128,8 +140,8 @@ Only the assigned agent may write to its own assignment folder.
 - `pending` + unmet dependencies = structural wait (automatic, no action needed)
 - `blocked` = runtime obstacle requiring human intervention (must set `blockedReason`)
 
-### Mission Status Rollup (computed, first-match-wins)
-1. `archived: true` in mission.md → `archived`
+### Project Status Rollup (computed, first-match-wins)
+1. `archived: true` in project.md → `archived`
 2. ALL assignments `completed` → `completed`
 3. ANY `in_progress` or `review` → `active`
 4. ANY `failed` → `failed`
@@ -151,31 +163,37 @@ Only the assigned agent may write to its own assignment folder.
 | `syntaur setup-adapter <framework>` | Generate adapter files for cursor, codex, or opencode |
 | `syntaur uninstall [--all]` | Remove plugins and optionally `~/.syntaur` data |
 
-### Mission & Assignment Creation
+### Project & Assignment Creation
+| Command | Description |
+|---------|-------------|
+| `syntaur create-project <title> [--slug S] [--dir D]` | Create new project with full scaffolding |
+| `syntaur create-assignment <title> --project M [--priority P] [--depends-on D] [--slug S] [--type T]` | Create assignment in a project |
+| `syntaur create-assignment <title> --one-off [--type T]` | Create standalone assignment at `~/.syntaur/assignments/<uuid>/` (project: null, slug display-only) |
+
+### Coordination (CLI-mediated writes)
 | Command | Description |
 |---------|-------------|
-| `syntaur create-mission <title> [--slug S] [--dir D]` | Create new mission with full scaffolding |
-| `syntaur create-assignment <title> --mission M [--priority P] [--depends-on D] [--slug S]` | Create assignment in a mission |
-| `syntaur create-assignment <title> --one-off` | Create standalone one-off assignment |
+| `syntaur comment <slug-or-uuid> "body" --type question\|note\|feedback [--reply-to <id>] [--project <slug>]` | Append to `comments.md`. Questions carry a resolve flag toggleable in the dashboard. |
+| `syntaur request <target> "text" [--from <source>] [--project <slug>]` | Append a todo to another assignment's `## Todos`, annotated `(from: <source>)`. |
 
 ### State Transitions
 | Command | Description |
 |---------|-------------|
-| `syntaur assign <slug> --agent <name> --mission <mission>` | Set assignee |
-| `syntaur start <slug> --mission <mission>` | pending → in_progress |
-| `syntaur review <slug> --mission <mission>` | in_progress → review |
-| `syntaur complete <slug> --mission <mission>` | in_progress/review → completed |
-| `syntaur block <slug> --mission <mission> --reason <text>` | → blocked |
-| `syntaur unblock <slug> --mission <mission>` | blocked → in_progress |
-| `syntaur fail <slug> --mission <mission>` | → failed |
-| `syntaur reopen <slug> --mission <mission>` | completed/failed → in_progress |
+| `syntaur assign <slug> --agent <name> --project <project>` | Set assignee |
+| `syntaur start <slug> --project <project>` | pending → in_progress |
+| `syntaur review <slug> --project <project>` | in_progress → review |
+| `syntaur complete <slug> --project <project>` | in_progress/review → completed |
+| `syntaur block <slug> --project <project> --reason <text>` | → blocked |
+| `syntaur unblock <slug> --project <project>` | blocked → in_progress |
+| `syntaur fail <slug> --project <project>` | → failed |
+| `syntaur reopen <slug> --project <project>` | completed/failed → in_progress |
 
 ### Session Tracking
 | Command | Description |
 |---------|-------------|
-| `syntaur track-session --mission M --assignment A --agent N` | Register agent session |
+| `syntaur track-session --project M --assignment A --agent N` | Register agent session |
 
-All commands support `--dir <path>` to override the default `~/.syntaur/missions/` directory.
+All commands support `--dir <path>` to override the default `~/.syntaur/projects/` directory.
 
 ---
 
@@ -192,7 +210,7 @@ plugin/
   skills/
     syntaur-protocol/SKILL.md    # Core protocol rules (background)
     grab-assignment/SKILL.md     # Claim a pending assignment
-    create-mission/SKILL.md      # Create new mission
+    create-project/SKILL.md      # Create new project
     create-assignment/SKILL.md   # Create new assignment
     plan-assignment/SKILL.md     # Write implementation plan
     complete-assignment/SKILL.md # Handoff and complete
@@ -212,17 +230,17 @@ plugin/
 | Skill | Trigger | Purpose |
 |-------|---------|---------|
 | `/syntaur-protocol` | Background — auto-loaded when working with Syntaur files | Core write boundary rules and protocol knowledge |
-| `/grab-assignment` | User says "grab assignment" or starts work on a mission | Discover pending assignments, claim one, create context.json |
-| `/create-mission` | User wants to create a new mission | Run CLI scaffolding, guide through editing mission files |
-| `/create-assignment` | User wants to add an assignment to a mission | Create assignment with all supporting files |
-| `/plan-assignment` | User wants to plan current assignment | Explore workspace, write detailed plan.md |
+| `/grab-assignment` | User says "grab assignment" or starts work on a project | Discover pending assignments, claim one, create context.json |
+| `/create-project` | User wants to create a new project | Run CLI scaffolding, guide through editing project files |
+| `/create-assignment` | User wants to add an assignment to a project | Create assignment with all supporting files |
+| `/plan-assignment` | User wants to plan current assignment | Explore workspace, write the next `plan-v<N>.md`, append a linked todo to `## Todos` (supersede prior plan todo) |
 | `/complete-assignment` | User is done with assignment work | Verify criteria, write handoff, transition state, close session |
 
 ### Hooks
 
 | Hook | Event | Behavior |
 |------|-------|----------|
-| PostToolUse: ExitPlanMode | User exits plan mode | Prompts to update plan.md with the plan just created |
+| PostToolUse: ExitPlanMode | User exits plan mode | Prompts to write the plan to the next unused `plan-v<N>.md` (or `plan.md` if none exists) and append a linked todo in the `## Todos` section of `assignment.md` |
 | SessionEnd | Claude Code session exits | Runs session-cleanup.sh to mark session as stopped |
 | PreToolUse: enforce-boundaries | Edit/Write/MultiEdit | Validates target path is within assignment boundaries |
 
@@ -240,27 +258,27 @@ syntaur                    # Dashboard is the default command
 ```
 
 ### Features
-- **Overview page:** Mission stats, quick actions, attention items
-- **Mission detail:** Assignment listing, resources, memories, status
+- **Overview page:** Project stats, quick actions, attention items
+- **Project detail:** Assignment listing, resources, memories, status
 - **Assignment detail:** Full assignment view with all fields, criteria checklist
 - **Kanban board:** Drag assignments between status columns
 - **Agent sessions:** Track active/completed/stopped agent sessions
 - **Server tracking:** Discover running dev servers via tmux session scanning
 - **Real-time updates:** WebSocket pushes file changes to the browser
-- **Markdown editing:** Edit mission.md, assignment.md, plan.md, scratchpad.md in-browser
+- **Markdown editing:** Edit project.md, assignment.md, plan files, scratchpad.md in-browser
 - **Attention queue:** Highlights blocked, failed, and review-pending items
 
 ### API Endpoints
 - `GET /api/overview` — Dashboard summary stats
-- `GET /api/missions` — List all missions
-- `GET /api/missions/:slug` — Mission detail with assignments
-- `GET /api/missions/:slug/assignments/:aslug` — Assignment detail
-- `GET /api/assignments` — All assignments across missions
+- `GET /api/projects` — List all projects
+- `GET /api/projects/:slug` — Project detail with assignments
+- `GET /api/projects/:slug/assignments/:aslug` — Assignment detail
+- `GET /api/assignments` — All assignments across projects
 - `GET /api/attention` — Items needing attention
 - `GET /api/agent-sessions` — Agent session list
-- `POST /api/missions` — Create mission
-- `POST /api/missions/:slug/assignments` — Create assignment
-- `PATCH /api/missions/:slug/assignments/:aslug` — Update assignment
+- `POST /api/projects` — Create project
+- `POST /api/projects/:slug/assignments` — Create assignment
+- `PATCH /api/projects/:slug/assignments/:aslug` — Update assignment
 - WebSocket at `/ws` for real-time file change notifications
 
 ### Architecture
@@ -276,9 +294,9 @@ syntaur                    # Dashboard is the default command
 Syntaur supports Cursor, Codex, and OpenCode via generated adapter files.
 
 ```bash
-syntaur setup-adapter cursor --mission <slug> --assignment <slug>
-syntaur setup-adapter codex --mission <slug> --assignment <slug>
-syntaur setup-adapter opencode --mission <slug> --assignment <slug>
+syntaur setup-adapter cursor --project <slug> --assignment <slug>
+syntaur setup-adapter codex --project <slug> --assignment <slug>
+syntaur setup-adapter opencode --project <slug> --assignment <slug>
 ```
 
 | Framework | Generated Files | Discovery |
@@ -295,25 +313,29 @@ Adapters embed protocol knowledge (write boundaries, lifecycle states, CLI comma
 
 ### Frontmatter Fields by File Type
 
-**assignment.md:** id, slug, title, status, priority, created, updated, assignee, externalIds, dependsOn, blockedReason, workspace (repository, worktreePath, branch, parentBranch), tags
+**assignment.md:** id, slug, title, **project (slug or null)**, **type (string or null)**, status, priority, created, updated, assignee, externalIds, dependsOn, blockedReason, workspace (repository, worktreePath, branch, parentBranch), tags
 
-**plan.md:** assignment, status (draft/approved/in_progress/completed), created, updated
+**plan files (plan.md, plan-v2.md, ...):** assignment, status (draft/approved/in_progress/completed), created, updated — zero or more per assignment, each linked from a todo in `assignment.md`'s `## Todos` section
+
+**progress.md:** assignment, entryCount, generated, updated — body is reverse-chron `## <timestamp>` entries
+
+**comments.md:** assignment, entryCount, generated, updated — body entries are `## <id>` with structured metadata lines (Recorded, Author, Type, optional Reply to, optional Resolved)
 
 **handoff.md:** assignment, updated, handoffCount
 
 **decision-record.md:** assignment, updated, decisionCount
 
-**mission.md:** id, slug, title, archived, archivedAt, archivedReason, created, updated, externalIds, tags
+**project.md:** id, slug, title, archived, archivedAt, archivedReason, created, updated, externalIds, tags
 
-**manifest.md:** version, mission, generated
+**manifest.md:** version, project, generated
 
-**_status.md:** mission, generated, status, progress (total/completed/in_progress/blocked/pending/review/failed), needsAttention (blockedCount/failedCount/unansweredQuestions)
+**_status.md:** project, generated, status, progress (total/completed/in_progress/blocked/pending/review/failed), needsAttention (blockedCount/failedCount/**openQuestions**). `openQuestions` is counted from every assignment's `comments.md` (entries where `Type: question` and `Resolved: false` or absent).
 
 ### Conventions
 - **Timestamps:** RFC 3339 / ISO 8601 with UTC: `2026-03-18T14:30:00Z`
 - **Paths:** Absolute expanded form in YAML (never `~`), relative in markdown links
-- **Slugs:** Lowercase, hyphen-separated, match folder names
-- **Protocol version:** `"1.0"` (string, not number)
+- **Slugs:** Lowercase, hyphen-separated, match folder names (project-nested). For standalone assignments, the folder is named by UUID and `slug` is display-only.
+- **Protocol version:** `"2.0"` (string, not number)
 
 ---
 
@@ -324,12 +346,12 @@ Adapters embed protocol knowledge (write boundaries, lifecycle states, CLI comma
 # 1. Run guided setup
 npx syntaur@latest setup
 
-# 2. Create your first mission
-syntaur create-mission "My First Mission"
+# 2. Create your first project
+syntaur create-project "My First Project"
 
 # 3. Create assignments
-syntaur create-assignment "Design the schema" --mission my-first-mission --priority high
-syntaur create-assignment "Implement the API" --mission my-first-mission --depends-on design-the-schema
+syntaur create-assignment "Design the schema" --project my-first-project --priority high
+syntaur create-assignment "Implement the API" --project my-first-project --depends-on design-the-schema
 
 # 4. Start the dashboard
 syntaur dashboard
@@ -338,7 +360,7 @@ syntaur dashboard
 ### Agent Workflow
 ```bash
 # In Claude Code, use skills:
-/grab-assignment my-first-mission       # Claim a pending assignment
+/grab-assignment my-first-project       # Claim a pending assignment
 /plan-assignment                         # Write implementation plan
 # ... do the work ...
 /complete-assignment                     # Handoff and complete
@@ -351,10 +373,10 @@ syntaur dashboard
 Created by `/grab-assignment` in the current working directory. Contains:
 ```json
 {
-  "missionSlug": "my-first-mission",
+  "projectSlug": "my-first-project",
   "assignmentSlug": "design-the-schema",
-  "missionDir": "/Users/you/.syntaur/missions/my-first-mission",
-  "assignmentDir": "/Users/you/.syntaur/missions/my-first-mission/assignments/design-the-schema",
+  "projectDir": "/Users/you/.syntaur/projects/my-first-project",
+  "assignmentDir": "/Users/you/.syntaur/projects/my-first-project/assignments/design-the-schema",
   "workspaceRoot": "/Users/you/projects/my-app",
   "title": "Design the schema",
   "branch": "feature/design-the-schema",
@@ -370,13 +392,19 @@ Read by `/plan-assignment`, `/complete-assignment`, and the write boundary hook
 ## Common Questions
 
 **Q: How do I see what assignments are available?**
-A: Use `/grab-assignment <mission-slug>` — it lists pending assignments. Or check the dashboard, or read `_index-assignments.md`.
+A: Use `/grab-assignment <project-slug>` — it lists pending assignments. Or check the dashboard, or read `_index-assignments.md`.
 
 **Q: Can two agents work on the same assignment?**
 A: No. Single-writer guarantee — one agent per assignment folder. Use separate assignments for parallel work.
 
 **Q: What if I need to ask the human a question?**
-A: Add it to the Q&A section of assignment.md. Do NOT set status to `blocked` for questions — `blocked` is for runtime obstacles only.
+A: Run `syntaur comment <slug> "question text" --type question`. It appends to `comments.md`, which replaces the old `## Questions & Answers` body section. The question rolls up into `_status.md`'s `openQuestions` counter and shows on the dashboard. Do NOT set status to `blocked` for questions — `blocked` is for runtime obstacles only.
+
+**Q: What goes in `progress.md` vs `handoff.md`?**
+A: `progress.md` is a continuous reverse-chron log of what you've done — append an entry per meaningful work unit. `handoff.md` is only written when you hand off work (to another agent or human), and summarizes the state at that transition.
+
+**Q: How do I route work to another assignment without breaking the single-writer rule?**
+A: Run `syntaur request <target> "text"` — it appends a todo to the target's `## Todos` annotated `(from: <source>)`. This is a CLI-mediated exception to the single-writer rule.
 
 **Q: How do indexes get updated?**
 A: Derived files are rebuilt by tooling. They are projections of assignment frontmatter. When divergence occurs, re-run rebuild.

package/platforms/claude-code/commands/doctor-syntaur/doctor-syntaur.md

@@ -0,0 +1,112 @@
+---
+name: doctor-syntaur
+description: Diagnose and help recover from common Syntaur bad states
+arguments:
+  - name: args
+    description: "Optional flags: --verbose, --only <check-id>"
+    required: false
+---
+
+# /doctor-syntaur
+
+Run `syntaur doctor` and help the user interpret the results, remediating issues where appropriate. Respect Syntaur write boundaries throughout.
+
+## Usage
+
+- `/doctor-syntaur` — run all checks
+- `/doctor-syntaur --verbose` — include passing checks in the summary
+- `/doctor-syntaur --only <check-id>` — re-run one check after remediation (e.g. `--only assignment.workspace-missing`)
+
+## Instructions
+
+When the user runs this command:
+
+### Step 1: Parse arguments
+
+From the argument string, extract optional flags:
+
+- `--verbose` — pass through to the CLI and include passing checks in the summary
+- `--only <check-id>` — pass through to the CLI to restrict to a single check
+
+### Step 2: Run the CLI and capture output + exit code
+
+Exit code 1 is expected (means issues were found). Do NOT let a non-zero exit fail the turn. Use a pattern like:
+
+```bash
+output=$(syntaur doctor --json [--only <check-id>] 2>&1); exit_code=$?
+```
+
+Then parse `$output` as JSON. If the JSON fails to parse, surface the raw output — that means the CLI itself broke.
+
+### Step 3: Handle exit codes and severity
+
+- **Exit 2** — Syntaur isn't initialized. Tell the user to run `syntaur init` and stop.
+- **Exit 1** (one or more errors) — continue to step 4; report both errors and warnings.
+- **Exit 0 and `summary.warn === 0`** — everything passed. Say so in one line (e.g. "All checks passed — no issues found.") and stop.
+- **Exit 0 and `summary.warn > 0`** — no errors but warnings exist. Continue to step 4; report the warnings. The CLI only exits 1 on errors, so warn-only runs still need to be surfaced to the user.
+
+### Step 4: Summarize results
+
+Group the `checks` array from the JSON by `category`. For each category:
+
+- Show errors first, then warnings.
+- Skip passes unless `--verbose` was passed.
+- Always include the `check.id` so the user can reference a specific issue in follow-up.
+
+Format each issue like:
+
+```
+[category] check.id — title
+  detail line
+  affected: path (truncate long lists)
+  fix: remediation.suggestion
+```
+
+### Step 5: Establish your write boundary (before offering any edit)
+
+Doctor reports issues from anywhere under `~/.syntaur/`. You are NOT allowed to edit most of those files. Before offering any remediation edit, compute your current write boundary:
+
+1. Read `.syntaur/context.json` in the current working directory (the same `cwd` you ran the CLI from).
+2. If the file does not exist, or exists but has no assignment fields (`projectSlug`, `assignmentSlug`, `projectDir`, `assignmentDir`):
+   - You have NO assignment context.
+   - Your only permitted edit target is the literal file `<cwd>/.syntaur/context.json` itself.
+   - For every other issue, show the `suggestion` text verbatim and do NOT offer to edit.
+3. If the file has assignment fields, record these paths:
+   - `assignmentDir` — your per-assignment write zone.
+   - `workspaceRoot` — your code write zone (may be absent).
+   - `<cwd>/.syntaur/context.json` — always editable.
+
+### Step 6: Offer remediation (issue by issue)
+
+For each error or warning, determine what kind of offer is appropriate.
+
+**First, use `remediation.kind`:**
+
+- **`auto-safe`** — offer to run `syntaur doctor --fix --only <id>`. Ask the user to confirm before running. (v1 has no auto-safe remediations yet — this is a placeholder for future versions.)
+- **`auto-destructive`** — never auto-run. Describe the impact and wait for the user.
+- **`manual`** — apply the path check below before offering an edit.
+
+**For `manual` remediations, compare each path in `affected[]` against your boundary from Step 5:**
+
+1. Let `allowed = [assignmentDir, workspaceRoot, <cwd>/.syntaur/context.json]` (dropping any undefined entries).
+2. A path is within boundary if and only if it equals `<cwd>/.syntaur/context.json` OR it is a strict path-prefix descendant of `assignmentDir` or `workspaceRoot`. Use path-segment comparison, not substring matching.
+3. If **every** path in `affected[]` is within boundary, you may offer to make the edit. Show a diff first; wait for confirmation; then write.
+4. If **any** path in `affected[]` is outside your boundary, do NOT offer to edit. Show the `suggestion` text verbatim and tell the user they or another tool must apply it.
+
+**Hard stop list — never write to these regardless of what doctor reports:**
+
+- `project.md`, `agent.md`, `claude.md`, `manifest.md`, `_status.md`
+- Any file starting with `_index-` or ending in `_index.md`
+- Any file in a project's `resources/` or `memories/` directory
+- Any file inside a different assignment's folder (i.e. `projects/<m>/assignments/<other>/...` where `<other> !== assignmentSlug`)
+
+### Step 7: Suggest a follow-up
+
+After proposing fixes, suggest the user re-run `/doctor-syntaur --only <check-id>` (or the whole command) to verify that issues resolved.
+
+## Guardrails
+
+- Always invoke `syntaur doctor --json`. Do not re-derive checks from the filesystem yourself.
+- Never pass `--fix` without explicit user confirmation.
+- Always show each issue's `check.id` so the user can reference it.
+- If the CLI output isn't valid JSON, show the raw output and stop — something is wrong with the install.

package/platforms/claude-code/commands/track-session/track-session.md

@@ -3,20 +3,20 @@ name: track-session
 description: Register this Claude Code session as an agent session in the Syntaur dashboard
 arguments:
   - name: args
-    description: "Optional flags: --description, --mission, --assignment"
+    description: "Optional flags: --description, --project, --assignment"
     required: false
 ---
 
 # /track-session
 
-Register the current Claude Code session as an agent session in the Syntaur dashboard. Works standalone or linked to a mission/assignment.
+Register the current Claude Code session as an agent session in the Syntaur dashboard. Works standalone or linked to a project/assignment.
 
 ## Usage
 
 - `/track-session` — register a standalone session
 - `/track-session --description "exploring auth patterns"` — with a description
-- `/track-session --mission <slug> --assignment <slug>` — linked to a mission
-- `/track-session --description "auth work" --mission <slug> --assignment <slug>` — both
+- `/track-session --project <slug> --assignment <slug>` — linked to a project
+- `/track-session --description "auth work" --project <slug> --assignment <slug>` — both
 
 ## Instructions
 
@@ -26,7 +26,7 @@ When the user runs this command:
 
 Extract optional flags from the argument string:
 - `--description "<text>"` or `--description <text>` — session description
-- `--mission <slug>` — mission to link to
+- `--project <slug>` — project to link to
 - `--assignment <slug>` — assignment to link to
 
 ### Step 2: Run the CLI command
@@ -34,14 +34,14 @@ Extract optional flags from the argument string:
 Run the track-session CLI command via Bash (use `dangerouslyDisableSandbox: true` since it writes to `~/.syntaur/`):
 
 ```bash
-syntaur track-session --agent claude --path $(pwd) [--description "<text>"] [--mission <slug>] [--assignment <slug>]
+syntaur track-session --agent claude --path $(pwd) [--description "<text>"] [--project <slug>] [--assignment <slug>]
 ```
 
 ### Step 3: Parse the session ID
 
 The CLI output will be one of:
 - `Registered standalone agent session <sessionId>.`
-- `Registered agent session <sessionId> for <assignment> in <mission>.`
+- `Registered agent session <sessionId> for <assignment> in <project>.`
 
 Extract the session ID from the output.
 
@@ -62,4 +62,4 @@ Write the session ID to `.syntaur/context.json` so the SessionEnd hook can mark
 Tell the user:
 - The session was registered (include the short session ID)
 - It will be auto-stopped when this conversation ends
-- If linked to a mission, mention which mission/assignment
+- If linked to a project, mention which project/assignment

package/platforms/claude-code/hooks/enforce-boundaries.sh

@@ -64,7 +64,7 @@ fi
 
 # --- Step 8: Read context ---
 ASSIGNMENT_DIR=$(jq -r '.assignmentDir // empty' "$CONTEXT_FILE" 2>/dev/null)
-MISSION_DIR=$(jq -r '.missionDir // empty' "$CONTEXT_FILE" 2>/dev/null)
+MISSION_DIR=$(jq -r '.projectDir // empty' "$CONTEXT_FILE" 2>/dev/null)
 WORKSPACE_ROOT=$(jq -r '.workspaceRoot // empty' "$CONTEXT_FILE" 2>/dev/null)
 
 if [ -z "$ASSIGNMENT_DIR" ] || [ -z "$MISSION_DIR" ]; then
@@ -88,7 +88,7 @@ if [[ "$FILE_PATH" == "$ASSIGNMENT_DIR"/* ]]; then
   allow_and_exit
 fi
 
-# Allow: files in mission resources/ directory (but NOT derived _index.md)
+# Allow: files in project resources/ directory (but NOT derived _index.md)
 if [[ "$FILE_PATH" == "$MISSION_DIR/resources/"* ]]; then
   BASENAME=$(basename "$FILE_PATH")
   if [[ "$BASENAME" == _* ]]; then
@@ -99,7 +99,7 @@ if [[ "$FILE_PATH" == "$MISSION_DIR/resources/"* ]]; then
   fi
 fi
 
-# Allow: files in mission memories/ directory (but NOT derived _index.md)
+# Allow: files in project memories/ directory (but NOT derived _index.md)
 if [[ "$FILE_PATH" == "$MISSION_DIR/memories/"* ]]; then
   BASENAME=$(basename "$FILE_PATH")
   if [[ "$BASENAME" == _* ]]; then
@@ -122,7 +122,7 @@ if [ -n "$WORKSPACE_ROOT" ] && [[ "$FILE_PATH" == "$WORKSPACE_ROOT"/* ]]; then
 fi
 
 # --- Step 11: Block the write ---
-REASON="Syntaur write boundary violation: Cannot write to '$FILE_PATH'. Allowed paths: assignment dir ($ASSIGNMENT_DIR), mission resources/memories, workspace ($WORKSPACE_ROOT)."
+REASON="Syntaur write boundary violation: Cannot write to '$FILE_PATH'. Allowed paths: assignment dir ($ASSIGNMENT_DIR), project resources/memories, workspace ($WORKSPACE_ROOT)."
 
 # Escape for JSON
 REASON_ESCAPED=$(echo "$REASON" | jq -Rs '.' 2>/dev/null)

package/platforms/claude-code/hooks/hooks.json

@@ -7,7 +7,7 @@
         "hooks": [
           {
             "type": "prompt",
-            "prompt": "You just exited plan mode. If there is an active Syntaur assignment (check for a workspace field in assignment.md), update the assignment's plan.md with the plan you just created and update assignment.md to reflect that planning is complete."
+            "prompt": "You just exited plan mode. If there is an active Syntaur assignment (check for a workspace field in assignment.md), pick the next unused `plan-v<N>.md` filename (or `plan.md` if no plan*.md exists yet) under the assignment dir, write the plan you just created there, and append a `- [ ] Execute [plan](./plan.md)` (or versioned equivalent, e.g. `- [ ] Execute [plan v2](./plan-v2.md)`) entry to the `## Todos` section of assignment.md — marking any prior active plan todo as superseded (`- [x] ~~...~~ (superseded by plan-v<N>)`). Never delete superseded todos."
           }
         ]
       }

package/platforms/claude-code/hooks/session-cleanup.sh

@@ -31,14 +31,14 @@ fi
 
 # --- Step 4: Extract context info ---
 SESSION_ID=$(jq -r '.sessionId // empty' "$CONTEXT_FILE" 2>/dev/null)
-MISSION_SLUG=$(jq -r '.missionSlug // empty' "$CONTEXT_FILE" 2>/dev/null)
+MISSION_SLUG=$(jq -r '.projectSlug // empty' "$CONTEXT_FILE" 2>/dev/null)
 ASSIGNMENT_SLUG=$(jq -r '.assignmentSlug // empty' "$CONTEXT_FILE" 2>/dev/null)
 
 PORT=$(cat "$HOME/.syntaur/dashboard-port" 2>/dev/null || echo "4800")
 
-# --- Step 5: If no session was registered, try to auto-register (requires mission+assignment) ---
+# --- Step 5: If no session was registered, try to auto-register (requires project+assignment) ---
 if [ -z "$SESSION_ID" ]; then
-  # Can only auto-register if we have mission and assignment context
+  # Can only auto-register if we have project and assignment context
   if [ -z "$MISSION_SLUG" ] || [ -z "$ASSIGNMENT_SLUG" ]; then
     exit 0
   fi
@@ -50,7 +50,7 @@ if [ -z "$SESSION_ID" ]; then
 
   RESPONSE=$(curl -sf -X POST "http://localhost:${PORT}/api/agent-sessions" \
     -H "Content-Type: application/json" \
-    -d "{\"missionSlug\": \"${MISSION_SLUG}\", \"assignmentSlug\": \"${ASSIGNMENT_SLUG}\", \"agent\": \"claude\", \"sessionId\": \"${SESSION_ID}\", \"path\": \"${CWD}\"}" \
+    -d "{\"projectSlug\": \"${MISSION_SLUG}\", \"assignmentSlug\": \"${ASSIGNMENT_SLUG}\", \"agent\": \"claude\", \"sessionId\": \"${SESSION_ID}\", \"path\": \"${CWD}\"}" \
     2>/dev/null) || true
 
   # If registration succeeded, update the context file with the session ID
@@ -63,7 +63,7 @@ fi
 # --- Step 6: Mark session as stopped via dashboard API ---
 BODY="{\"status\": \"stopped\"}"
 if [ -n "$MISSION_SLUG" ]; then
-  BODY="{\"status\": \"stopped\", \"missionSlug\": \"${MISSION_SLUG}\"}"
+  BODY="{\"status\": \"stopped\", \"projectSlug\": \"${MISSION_SLUG}\"}"
 fi
 
 curl -sf -X PATCH "http://localhost:${PORT}/api/agent-sessions/${SESSION_ID}/status" \

package/platforms/claude-code/references/file-ownership.md

@@ -6,9 +6,7 @@ Agents must NEVER modify these files:
 
 | File | Location |
 |------|----------|
-| `mission.md` | `<mission>/mission.md` |
-| `agent.md` | `<mission>/agent.md` |
-| `claude.md` | `<mission>/claude.md` |
+| `project.md` | `<project>/project.md` |
 
 ## Agent-Writable (YOUR assignment folder ONLY)
 
@@ -16,20 +14,34 @@ You may ONLY write to files inside your assigned assignment folder:
 
 | File | Purpose |
 |------|---------|
-| `assignment.md` | Assignment record, source of truth for state |
-| `plan.md` | Your implementation plan |
+| `assignment.md` | Assignment record, source of truth for state (includes `## Todos` checklist) |
+| `plan*.md` | Versioned implementation plans (optional, 0 or more: `plan.md`, `plan-v2.md`, ...) — each linked from a todo in `assignment.md` |
+| `progress.md` | Append-only timestamped progress log (newest first). Replaces the old `## Progress` body section. |
 | `scratchpad.md` | Working notes |
 | `handoff.md` | Append-only handoff log |
 | `decision-record.md` | Append-only decision log |
 
-Path pattern: `~/.syntaur/missions/<mission>/assignments/<your-assignment>/`
+Path pattern (project-nested): `~/.syntaur/projects/<project>/assignments/<your-assignment>/`
+Path pattern (standalone): `~/.syntaur/assignments/<your-assignment-uuid>/`
+
+## CLI-Mediated Shared-Writable
+
+Do NOT edit these files directly. Use the listed CLI commands:
+
+| File | Mediator |
+|------|----------|
+| `comments.md` (any assignment) | `syntaur comment <slug-or-uuid> "body" [--type question\|note\|feedback] [--reply-to <id>]` |
+| `## Todos` in another assignment's `assignment.md` (cross-assignment request) | `syntaur request <source> <target> "text"` |
+| Question resolution | `PATCH /api/.../comments/:id/resolved` (dashboard) or toggle in dashboard UI |
+
+These are bounded exceptions to the single-writer rule for assignment folders — the CLI serializes writes to avoid conflicts.
 
 ## Shared-Writable (any agent or human)
 
 | Location | Purpose |
 |----------|---------|
-| `<mission>/resources/<slug>.md` | Reference material |
-| `<mission>/memories/<slug>.md` | Learnings and patterns |
+| `<project>/resources/<slug>.md` | Reference material |
+| `<project>/memories/<slug>.md` | Learnings and patterns |
 
 ## Derived (NEVER edit)