@cleocode/cleo 2026.2.5 → 2026.2.7

package/packages/ct-skills/skills/_shared/manifest-operations.md

@@ -0,0 +1,810 @@
+# Manifest Operations Reference
+
+**Provenance**: T3154 (Epic: T3147) - Single-source reference for all manifest operations
+**Status**: ACTIVE
+**Version**: 1.0.0
+
+This reference defines all CLI operations for managing the agent outputs manifest (`MANIFEST.jsonl`). Skills and protocols SHOULD reference this file instead of duplicating JSONL instructions.
+
+---
+
+## Overview
+
+The manifest system provides O(1) append operations and race-condition-free concurrent writes through JSONL format. Each line is a complete JSON object representing one research/output entry.
+
+**Default Paths**:
+- Output directory: `claudedocs/agent-outputs/` (configurable via `agentOutputs.directory`)
+- Manifest file: `MANIFEST.jsonl` (configurable via `agentOutputs.manifestFile`)
+- Full path: `{{OUTPUT_DIR}}/{{MANIFEST_PATH}}`
+
+**Design Principles**:
+- Append-only writes preserve audit trail
+- Single-line corruption doesn't corrupt entire file
+- Concurrent writes are safe (atomic line appends)
+- Orchestrators read manifest summaries, NOT full files
+
+---
+
+## CLI Commands
+
+### cleo research add
+
+Create a new manifest entry for agent output.
+
+**Usage**:
+```bash
+cleo research add \
+  --title "Entry Title" \
+  --file "path/to/output.md" \
+  --topics "topic1,topic2,topic3" \
+  --findings "Finding 1,Finding 2,Finding 3" \
+  [--status STATUS] \
+  [--task T####] \
+  [--epic T####] \
+  [--actionable | --not-actionable] \
+  [--needs-followup T001,T002] \
+  [--agent-type TYPE]
+```
+
+**Required Flags**:
+| Flag | Description | Example |
+|------|-------------|---------|
+| `--title` | Human-readable title | `"Authentication Research"` |
+| `--file` | Relative path to output file | `"2026-02-07_auth-research.md"` |
+| `--topics` | Comma-separated topic tags | `"authentication,security,jwt"` |
+| `--findings` | Comma-separated key findings (1-7 items) | `"JWT tokens expire after 1h,OAuth2 preferred,PKCE required"` |
+
+**Optional Flags**:
+| Flag | Default | Valid Values |
+|------|---------|--------------|
+| `--status` | `complete` | `complete`, `partial`, `blocked` |
+| `--task` | none | Task ID (e.g., `T1234`) |
+| `--epic` | none | Epic ID (e.g., `T1200`) |
+| `--actionable` | `true` | Boolean flag |
+| `--not-actionable` | - | Negates actionable |
+| `--needs-followup` | `[]` | Comma-separated task IDs |
+| `--agent-type` | `research` | See Agent Type Values below |
+
+**Agent Type Values** (RCSD-IVTR protocol + workflow types):
+- **Protocol types**: `research`, `consensus`, `specification`, `decomposition`, `implementation`, `contribution`, `release`
+- **Workflow types**: `validation`, `documentation`, `analysis`, `testing`, `cleanup`, `design`, `architecture`, `report`
+- **Extended types**: `synthesis`, `orchestrator`, `handoff`, `verification`, `review`
+- **Skill types**: Any `ct-*` prefix (e.g., `ct-orchestrator`)
+
+**Example**:
+```bash
+cleo research add \
+  --title "JWT Authentication Best Practices" \
+  --file "2026-02-07_jwt-auth.md" \
+  --topics "authentication,jwt,security" \
+  --findings "Use RS256 for asymmetric signing,Tokens expire in 1h,Refresh tokens stored securely" \
+  --status complete \
+  --task T3154 \
+  --actionable \
+  --agent-type research
+```
+
+**Output**: JSON with created entry ID
+```json
+{
+  "success": true,
+  "entryId": "jwt-auth-2026-02-07",
+  "manifestPath": "claudedocs/agent-outputs/MANIFEST.jsonl"
+}
+```
+
+---
+
+### cleo research update
+
+Update an existing manifest entry.
+
+**Usage**:
+```bash
+cleo research update <entry-id> \
+  [--title "New Title"] \
+  [--status STATUS] \
+  [--findings "F1,F2,F3"] \
+  [--topics "T1,T2"] \
+  [--actionable | --not-actionable] \
+  [--needs-followup T001,T002]
+```
+
+**Parameters**:
+- `<entry-id>`: Entry ID from manifest (e.g., `jwt-auth-2026-02-07`)
+
+**Flags**: Same as `add` command (all optional for update)
+
+**Example**:
+```bash
+cleo research update jwt-auth-2026-02-07 \
+  --status partial \
+  --needs-followup T3155,T3156
+```
+
+---
+
+### cleo research list
+
+Query and filter manifest entries.
+
+**Usage**:
+```bash
+cleo research list \
+  [--status STATUS] \
+  [--type TYPE] \
+  [--topic TOPIC] \
+  [--since DATE] \
+  [--limit N] \
+  [--actionable]
+```
+
+**Filter Options**:
+| Flag | Description | Example |
+|------|-------------|---------|
+| `--status` | Filter by status | `complete`, `partial`, `blocked`, `archived` |
+| `--type` | Filter by agent type | `research`, `implementation`, `validation` |
+| `--topic` | Filter by topic tag | `authentication` |
+| `--since` | Entries since date | `2026-02-01` (ISO 8601: YYYY-MM-DD) |
+| `--limit` | Max results | `20` (default: 20) |
+| `--actionable` | Only actionable entries | Boolean flag |
+
+**Example**:
+```bash
+# Recent research entries
+cleo research list --type research --since 2026-02-01 --limit 10
+
+# Actionable partial entries
+cleo research list --status partial --actionable
+```
+
+**Output**: JSON array with manifest entries
+```json
+{
+  "success": true,
+  "count": 3,
+  "entries": [
+    {
+      "id": "jwt-auth-2026-02-07",
+      "title": "JWT Authentication Best Practices",
+      "status": "complete",
+      "topics": ["authentication", "jwt", "security"],
+      "key_findings": ["Use RS256...", "Tokens expire...", "Refresh tokens..."]
+    }
+  ]
+}
+```
+
+---
+
+### cleo research show
+
+Display details of a specific manifest entry.
+
+**Usage**:
+```bash
+cleo research show <entry-id> [--full | --findings-only]
+```
+
+**Parameters**:
+- `<entry-id>`: Entry ID from manifest
+
+**Options**:
+| Flag | Description | Default |
+|------|-------------|---------|
+| `--findings-only` | Only show key_findings array | ✓ |
+| `--full` | Include full file content (WARNING: large context) | |
+
+**Example**:
+```bash
+# Minimal output (just key findings)
+cleo research show jwt-auth-2026-02-07
+
+# Full entry metadata
+cleo research show jwt-auth-2026-02-07 --full
+```
+
+**Output**: JSON with entry details
+```json
+{
+  "success": true,
+  "entry": {
+    "id": "jwt-auth-2026-02-07",
+    "file": "2026-02-07_jwt-auth.md",
+    "title": "JWT Authentication Best Practices",
+    "date": "2026-02-07",
+    "status": "complete",
+    "topics": ["authentication", "jwt", "security"],
+    "key_findings": [
+      "Use RS256 for asymmetric signing",
+      "Tokens expire in 1h",
+      "Refresh tokens stored securely"
+    ],
+    "actionable": true,
+    "needs_followup": [],
+    "linked_tasks": ["T3154"]
+  }
+}
+```
+
+---
+
+### cleo research link
+
+Link a research entry to a task (bidirectional association).
+
+**Usage**:
+```bash
+cleo research link <task-id> <research-id> [--notes "Custom note"]
+```
+
+**Parameters**:
+- `<task-id>`: Task ID (e.g., `T3154`)
+- `<research-id>`: Entry ID from manifest
+
+**Options**:
+| Flag | Description |
+|------|-------------|
+| `--notes` | Custom note text instead of default |
+
+**Example**:
+```bash
+cleo research link T3154 jwt-auth-2026-02-07
+cleo research link T3154 jwt-auth-2026-02-07 --notes "Primary research source"
+```
+
+**Effects**:
+- Adds research ID to task's `.linkedResearch` array
+- Adds task ID to manifest entry's `linked_tasks` array
+- Creates bidirectional reference for discovery
+
+**Verify Link**:
+```bash
+cleo show T3154  # Check .linkedResearch array
+cleo research show jwt-auth-2026-02-07  # Check linked_tasks
+```
+
+---
+
+### cleo research unlink
+
+Remove link between research and task.
+
+**Usage**:
+```bash
+cleo research unlink <task-id> <research-id>
+```
+
+**Example**:
+```bash
+cleo research unlink T3154 jwt-auth-2026-02-07
+```
+
+---
+
+### cleo research links
+
+Show all research linked to a specific task.
+
+**Usage**:
+```bash
+cleo research links <task-id>
+```
+
+**Example**:
+```bash
+cleo research links T3154
+```
+
+**Output**: JSON array of linked research entries
+
+---
+
+### cleo research pending
+
+Show entries with `needs_followup` (orchestrator handoffs).
+
+**Usage**:
+```bash
+cleo research pending [--brief]
+```
+
+**Options**:
+| Flag | Description |
+|------|-------------|
+| `--brief` | Minimal output (just IDs and followup tasks) |
+
+**Example**:
+```bash
+cleo research pending
+cleo research pending --brief
+```
+
+**Output**: JSON array of entries requiring followup
+```json
+{
+  "success": true,
+  "count": 2,
+  "entries": [
+    {
+      "id": "partial-research-2026-02-06",
+      "title": "Incomplete Analysis",
+      "status": "partial",
+      "needs_followup": ["T3155", "T3156"]
+    }
+  ]
+}
+```
+
+---
+
+### cleo research archive
+
+Archive old manifest entries to maintain context efficiency.
+
+**Usage**:
+```bash
+cleo research archive \
+  [--threshold BYTES] \
+  [--percent N] \
+  [--dry-run]
+```
+
+**Options**:
+| Flag | Default | Description |
+|------|---------|-------------|
+| `--threshold` | `200000` | Archive threshold in bytes (~50K tokens) |
+| `--percent` | `50` | Percentage of oldest entries to archive |
+| `--dry-run` | - | Show what would be archived without changes |
+
+**Example**:
+```bash
+# Preview archival
+cleo research archive --dry-run
+
+# Archive oldest 50% when manifest exceeds 200KB
+cleo research archive --threshold 200000 --percent 50
+```
+
+**Effects**:
+- Moves entries to `{{OUTPUT_DIR}}/archive/MANIFEST-archive.jsonl`
+- Updates status to `archived` in archive file
+- Removes from main manifest to reduce context size
+
+---
+
+### cleo research archive-list
+
+List entries from the archive file.
+
+**Usage**:
+```bash
+cleo research archive-list \
+  [--limit N] \
+  [--since DATE]
+```
+
+**Options**:
+| Flag | Default | Description |
+|------|---------|-------------|
+| `--limit` | `50` | Max entries to return |
+| `--since` | none | Filter archived since date (ISO 8601) |
+
+**Example**:
+```bash
+cleo research archive-list --limit 100 --since 2026-01-01
+```
+
+---
+
+### cleo research status
+
+Show manifest size and archival status.
+
+**Usage**:
+```bash
+cleo research status
+```
+
+**Output**: JSON with size metrics
+```json
+{
+  "success": true,
+  "manifest": {
+    "path": "claudedocs/agent-outputs/MANIFEST.jsonl",
+    "size": 153420,
+    "entryCount": 42,
+    "threshold": 200000,
+    "needsArchival": false
+  }
+}
+```
+
+---
+
+### cleo research stats
+
+Show comprehensive manifest statistics.
+
+**Usage**:
+```bash
+cleo research stats
+```
+
+**Output**: JSON with detailed statistics
+```json
+{
+  "success": true,
+  "stats": {
+    "totalEntries": 42,
+    "byStatus": {
+      "complete": 35,
+      "partial": 5,
+      "blocked": 2
+    },
+    "byAgentType": {
+      "research": 20,
+      "implementation": 15,
+      "validation": 7
+    },
+    "actionableCount": 38,
+    "needsFollowupCount": 7
+  }
+}
+```
+
+---
+
+### cleo research validate
+
+Validate manifest file integrity and entry format.
+
+**Usage**:
+```bash
+cleo research validate [--fix] [--protocol] [--task T####]
+```
+
+**Options**:
+| Flag | Description |
+|------|-------------|
+| `--fix` | Remove invalid entries (destructive) |
+| `--protocol` | Validate against protocol requirements |
+| `--task` | Validate entries linked to specific task |
+
+**Example**:
+```bash
+# Check integrity
+cleo research validate
+
+# Fix invalid entries
+cleo research validate --fix
+
+# Validate protocol compliance for task outputs
+cleo research validate --protocol --task T3154
+```
+
+**Validation Checks**:
+- Valid JSON syntax per line
+- Required fields present: `id`, `file`, `title`, `date`, `status`, `topics`, `key_findings`, `actionable`
+- Status enum: `complete`, `partial`, `blocked`, `archived`
+- Date format: ISO 8601 (YYYY-MM-DD)
+- Field types: `topics` array, `key_findings` array, `actionable` boolean
+- Agent type validity (protocol + workflow types)
+
+**Exit Codes**:
+- `0`: Validation passed
+- `6`: Validation errors found (`EXIT_VALIDATION_ERROR`)
+
+---
+
+### cleo research compact
+
+Remove duplicate/obsolete entries from manifest.
+
+**Usage**:
+```bash
+cleo research compact
+```
+
+**Effects**:
+- Removes duplicate entries (same ID)
+- Keeps most recent version of duplicates
+- Atomic operation with backup
+
+---
+
+### cleo research get
+
+Get single entry by ID (raw JSON object).
+
+**Usage**:
+```bash
+cleo research get <entry-id>
+```
+
+**Example**:
+```bash
+cleo research get jwt-auth-2026-02-07
+```
+
+**Output**: Raw JSON object (no wrapper)
+
+---
+
+### cleo research inject
+
+Output the subagent injection template for prompts.
+
+**Usage**:
+```bash
+cleo research inject [--raw] [--clipboard]
+```
+
+**Options**:
+| Flag | Description |
+|------|-------------|
+| `--raw` | Output template without variable substitution |
+| `--clipboard` | Copy to clipboard (pbcopy/xclip) |
+
+**Example**:
+```bash
+# Output with current values
+cleo research inject
+
+# Raw template with {{TOKENS}}
+cleo research inject --raw
+
+# Copy to clipboard
+cleo research inject --clipboard
+```
+
+---
+
+## Manifest Entry Schema
+
+### Required Fields
+
+| Field | Type | Description | Constraints |
+|-------|------|-------------|-------------|
+| `id` | string | Unique identifier | Format: `{topic-slug}-{date}` or `T####-{slug}` |
+| `file` | string | Output file path | Relative to manifest directory |
+| `title` | string | Human-readable title | Non-empty |
+| `date` | string | Entry creation date | ISO 8601: YYYY-MM-DD |
+| `status` | enum | Entry status | `complete`, `partial`, `blocked`, `archived` |
+| `topics` | array | Categorization tags | Array of strings |
+| `key_findings` | array | Key findings (1-7 items) | Array of strings, 1-7 items, one sentence each |
+| `actionable` | boolean | Requires action | `true` or `false` |
+
+### Optional Fields
+
+| Field | Type | Description | Default |
+|-------|------|-------------|---------|
+| `agent_type` | string | Agent/protocol type | `research` |
+| `needs_followup` | array | Task IDs requiring attention | `[]` |
+| `linked_tasks` | array | Associated task IDs | `[]` |
+| `audit` | object | Audit metadata (T2578) | See audit schema |
+
+### Audit Object Schema (v2.10.0+)
+
+When present, the `audit` field provides operational metadata:
+
+```json
+{
+  "audit": {
+    "created": {
+      "timestamp": "2026-02-07T05:00:00Z",
+      "agent": "cleo-subagent",
+      "taskId": "T3154"
+    },
+    "updated": {
+      "timestamp": "2026-02-07T06:00:00Z",
+      "agent": "ct-orchestrator",
+      "reason": "Status change to partial"
+    }
+  }
+}
+```
+
+---
+
+## Token Placeholders
+
+### Standard Tokens (Pre-Resolved)
+
+| Token | Description | Example |
+|-------|-------------|---------|
+| `{{TASK_ID}}` | Current task identifier | `T3154` |
+| `{{EPIC_ID}}` | Parent epic identifier | `T3147` |
+| `{{DATE}}` | Current date | `2026-02-07` |
+| `{{TOPIC_SLUG}}` | URL-safe topic name | `jwt-authentication` |
+| `{{OUTPUT_DIR}}` | Output directory | `claudedocs/agent-outputs` |
+| `{{MANIFEST_PATH}}` | Manifest filename | `MANIFEST.jsonl` |
+
+### Command Tokens (CLEO Defaults)
+
+| Token | Default Value |
+|-------|---------------|
+| `{{TASK_LINK_CMD}}` | `cleo research link` |
+| `{{TASK_COMPLETE_CMD}}` | `cleo complete` |
+| `{{TASK_START_CMD}}` | `cleo start` |
+| `{{TASK_SHOW_CMD}}` | `cleo show` |
+
+**Note**: Orchestrators MUST pre-resolve all tokens before spawning subagents. Subagents CANNOT resolve `@` references or `{{TOKEN}}` patterns.
+
+---
+
+## Usage in Protocols
+
+### Research Protocol Example
+
+```markdown
+## Output Requirements
+
+1. Write findings to `{{OUTPUT_DIR}}/{{DATE}}_{{TOPIC_SLUG}}.md`
+2. Create manifest entry:
+
+```bash
+cleo research add \
+  --title "{{TITLE}}" \
+  --file "{{DATE}}_{{TOPIC_SLUG}}.md" \
+  --topics "{{TOPICS_CSV}}" \
+  --findings "{{FINDINGS_CSV}}" \
+  --status complete \
+  --task {{TASK_ID}} \
+  --agent-type research
+```
+
+3. Link to task: `{{TASK_LINK_CMD}} {{TASK_ID}} {{ENTRY_ID}}`
+```
+
+### Implementation Protocol Example
+
+```markdown
+## Completion Sequence
+
+```bash
+# Write implementation file
+# ...
+
+# Record in manifest
+cleo research add \
+  --title "{{TASK_TITLE}} Implementation" \
+  --file "{{OUTPUT_FILE}}" \
+  --topics "{{TASK_LABELS}}" \
+  --findings "Implemented X,Added Y,Modified Z" \
+  --status complete \
+  --task {{TASK_ID}} \
+  --agent-type implementation
+
+# Complete task
+{{TASK_COMPLETE_CMD}} {{TASK_ID}}
+```
+```
+
+---
+
+## Anti-Patterns
+
+### ❌ Pretty-Printed JSON
+
+```bash
+# WRONG - Creates multiple lines
+echo '{
+  "id": "test",
+  "title": "Test"
+}' >> MANIFEST.jsonl
+```
+
+**Problem**: Breaks JSONL format (one object per line)
+
+**Solution**: Use `jq -c` for compact output
+```bash
+jq -nc '{id: "test", title: "Test"}' >> MANIFEST.jsonl
+```
+
+---
+
+### ❌ Direct File Writes
+
+```bash
+# WRONG - Bypasses validation
+echo "$json" >> claudedocs/agent-outputs/MANIFEST.jsonl
+```
+
+**Problem**: No validation, no atomic operation, no audit trail
+
+**Solution**: Use CLI commands
+```bash
+cleo research add --title "..." --file "..." --topics "..." --findings "..."
+```
+
+---
+
+### ❌ Missing Key Findings
+
+```bash
+# WRONG - Empty findings array
+cleo research add --findings ""
+```
+
+**Problem**: Manifest is for discovery - empty findings defeat purpose
+
+**Solution**: Always provide 1-7 concise findings
+```bash
+cleo research add --findings "Finding 1,Finding 2,Finding 3"
+```
+
+---
+
+### ❌ Returning Full Content
+
+```markdown
+**Subagent response:**
+
+Here is my research:
+
+# JWT Authentication
+
+[5000 words of content...]
+```
+
+**Problem**: Bloats orchestrator context window
+
+**Solution**: Return ONLY summary message
+```markdown
+Research complete. See MANIFEST.jsonl for summary.
+```
+
+---
+
+### ❌ Unresolved Tokens in Subagent
+
+```bash
+# WRONG - Subagent cannot resolve @file references
+cleo research add --findings "@findings.txt"
+```
+
+**Problem**: Subagents cannot resolve `@` or `{{TOKEN}}` patterns
+
+**Solution**: Orchestrator must pre-resolve
+```bash
+# Orchestrator resolves before spawn
+findings=$(cat findings.txt | tr '\n' ',' | sed 's/,$//')
+# Then passes to subagent as plain text
+```
+
+---
+
+### ❌ Skipping Task Link
+
+```bash
+# WRONG - No bidirectional association
+cleo research add --title "..." --file "..." --topics "..." --findings "..."
+# (missing --task flag)
+```
+
+**Problem**: Research orphaned, cannot be discovered from task
+
+**Solution**: Always link to task
+```bash
+cleo research add \
+  --title "..." \
+  --file "..." \
+  --topics "..." \
+  --findings "..." \
+  --task {{TASK_ID}}
+
+# Or link after creation
+cleo research link {{TASK_ID}} {{ENTRY_ID}}
+```
+
+---
+
+## References
+
+- **Task System Integration**: `@skills/_shared/task-system-integration.md`
+- **Subagent Protocol Base**: `@skills/_shared/subagent-protocol-base.md`
+- **Research Manifest Library**: `lib/research-manifest.sh`
+- **Research CLI**: `scripts/research.sh`
+- **Exit Codes**: `lib/exit-codes.sh` (EXIT_VALIDATION_ERROR = 6)
+- **RCSD-IVTR Protocol**: `docs/specs/PROJECT-LIFECYCLE-SPEC.md`