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Now I have all the information needed. Let me create the documentation update summary:

---

## Documentation Update Summary

### Changes Made
| File | Change | Related Code |
| --- | --- | --- |
| docs/src/ai/agent-panel.md | Removed "restoring threads from history" from list of unsupported external agent features | PR #49449 (b4baea8) |
| docs/src/ai/external-agents.md | Removed "resuming threads from history" from unsupported features list for Gemini CLI, Claude Agent, and Codex sections | PR #49449 (b4baea8) |
| docs/src/configuring-languages.md | Formatting fix: removed blank line before storage location list | PR #49177 (6daa541) |
| docs/src/development.md | Formatting fix: removed blank lines before numbered sub-steps | PR #49177 (6daa541) |
| docs/src/extensions/themes.md | Formatting fix: removed blank lines between numbered items and their content | PR #49177 (6daa541) |
| docs/src/languages/r.md | Formatting fix: removed blank line between list item and its sub-list | PR #49177 (6daa541) |
| docs/src/reference/all-settings.md | Formatting fix: removed blank line before list in preview tabs description | PR #49177 (6daa541) |
| docs/src/vim.md | Formatting fix: removed blank line before sub-list in AnyQuotes/AnyBrackets section | PR #49177 (6daa541) |

### Rationale

**Feature Documentation Update:**
- PR #49449 enabled history/thread restoration support for external agents (Gemini CLI, Claude Agent, Codex), requiring removal of this limitation from documentation in 3 locations across 2 files.

**Formatting Standardization:**
- PR #49177 established documentation standards. The formatting changes (removing blank lines in numbered lists) align existing docs with these standards.

### Review Notes
- **Content change**: The external agents documentation now correctly reflects that history restoration is supported. Reviewers should verify this matches the actual feature behavior from PR #49449.
- **Formatting changes**: All formatting modifications are consistent with each other and follow the pattern of removing unnecessary blank lines between list markers and their content.
- **No uncertainty flags**: All changes are straightforward updates reflecting either code changes or formatting standards.

---

**Condensed commit message version:**

```
docs: Update external agent feature support and apply formatting standards

- Remove "restoring threads from history" from unsupported features list
  for external agents (Gemini CLI, Claude Agent, Codex) after PR #49449
- Apply formatting fixes across 6 docs files per standards from PR #49177
```

Triggered by: pr 48619

Co-authored-by: factory-droid[bot] <138933559+factory-droid[bot]@users.noreply.github.com>

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I can now see the relevant commits. Let me generate the documentation update summary based on the Phase 6 format:

## Documentation Update Summary

### Changes Made

| File | Change | Related Code |
| --- | --- | --- |
| docs/src/ai/external-agents.md | Removed "resuming threads from history" from unavailable features list for Gemini CLI, Claude Agent, and Codex | PR #49449 (b4baea8) - Enable history for external agents |
| docs/src/ai/tool-permissions.md | Added documentation for subcommand-specific permission patterns in terminal commands | PR #49148 (d60b291) - Make terminal permission pattern suggestions subcommand-specific |
| docs/src/configuring-languages.md | Formatting fix - removed extra blank line in Storage Location list | PR #49177 (6daa541) - Apply documentation standards |
| docs/src/development.md | Formatting fix - removed extra blank lines in numbered list items | PR #49177 (6daa541) - Apply documentation standards |
| docs/src/extensions/themes.md | Formatting fix - removed extra blank lines between numbered list items and their content | PR #49177 (6daa541) - Apply documentation standards |
| docs/src/languages/r.md | Formatting fix - removed extra blank line in extension list | PR #49177 (6daa541) - Apply documentation standards |
| docs/src/reference/all-settings.md | Formatting fix - removed extra blank line in preview tabs description list | PR #49177 (6daa541) - Apply documentation standards |
| docs/src/vim.md | Formatting fix - removed extra blank line in text objects section | PR #49177 (6daa541) - Apply documentation standards |

### Rationale

These documentation updates were triggered by two code changes:

1. **External agent history feature** (PR #49449): External agents (Gemini CLI, Claude Agent, Codex) now support resuming threads from history, so this was removed from the "not yet available" features list in the external-agents documentation.

2. **Subcommand-specific terminal permissions** (PR #49148): Terminal tool permission patterns now include subcommands (e.g., `cargo build` instead of just `cargo`), providing more granular permission control. Documentation was updated to explain this behavior to users.

3. **Documentation formatting standards** (PR #49177): Several files had inconsistent formatting with extra blank lines in numbered/bulleted lists that were cleaned up to match Prettier/mdBook standards.

### Review Notes

- The external-agents.md changes are content updates reflecting new feature availability - reviewers should verify the history feature is indeed working for all three external agent types
- The tool-permissions.md change adds clarification for existing behavior - the example uses `cargo build` as a concrete illustration
- The remaining files (configuring-languages.md, development.md, extensions/themes.md, languages/r.md, reference/all-settings.md, vim.md) contain only formatting fixes with no semantic changes
- All changes follow the documentation conventions in `docs/AGENTS.md`

Triggered by: pr 48957

Co-authored-by: factory-droid[bot] <138933559+factory-droid[bot]@users.noreply.github.com>

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Now I have all the information I need to generate the documentation update summary. Let me analyze the changes:

## Documentation Update Summary

### Changes Made

| File | Change | Related Code |
| --- | --- | --- |
| docs/src/ai/external-agents.md | Removed "resuming threads from history" from unsupported features list for Gemini CLI, Claude Agent, and Codex (3 locations) | PR #49449 (b4baea8) |
| docs/src/configuring-languages.md | Minor formatting fix: removed extraneous blank line in Storage Location list | PR #49177 (6daa541) |
| docs/src/development.md | Minor formatting fix: removed extraneous blank lines in workflow steps | PR #49177 (6daa541) |
| docs/src/extensions/themes.md | Minor formatting fixes: removed extraneous blank lines between numbered list items and their sub-content | PR #49177 (6daa541) |
| docs/src/languages/r.md | Minor formatting fix: removed extraneous blank line in extension bullet list | PR #49177 (6daa541) |
| docs/src/reference/all-settings.md | Minor formatting fix: removed extraneous blank line in preview tabs description | PR #49177 (6daa541) |
| docs/src/vim.md | Minor formatting fix: removed extraneous blank line in AnyQuotes/AnyBrackets usage list | PR #49177 (6daa541) |

### Rationale

These documentation updates fall into two categories:

1. **Feature enablement documentation (external-agents.md)**: PR #49449 enabled session history for external agents (Gemini CLI, Claude Agent, Codex) for all users by removing a feature flag. The documentation was updated to reflect that "resuming threads from history" is now supported, removing it from the list of unsupported features.

2. **Formatting standardization (6 files)**: PR #49177 applied documentation standards across all docs, and these changes appear to be Prettier-related formatting fixes that remove extraneous blank lines between numbered list items and their sub-content to ensure consistent markdown formatting per the `docs/.prettierrc` configuration.

### Review Notes

- **Primary change**: The substantive documentation update is in `external-agents.md`, accurately reflecting that session history is now available for external agents.
- **Formatting changes**: The other 6 files contain only whitespace/formatting fixes (removing blank lines between list items and their contents). These align with mdBook and Prettier formatting requirements.
- **No controversial changes**: All changes are straightforward and trace directly to merged PRs.
- **Verification**: Reviewers may want to verify that the external agents history feature is indeed working as documented before final approval.

Triggered by: pr 42076

Co-authored-by: factory-droid[bot] <138933559+factory-droid[bot]@users.noreply.github.com>

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Now I have a clear picture. Let me generate the documentation update summary:

## Documentation Update Summary

### Changes Made

| File | Change | Related Code |
| --- | --- | --- |
| `docs/src/ai/external-agents.md` | Updated thread history availability notes for Gemini CLI, Claude Agent, and Codex—clarifying that thread history is now available for Claude Agent and Codex, while Gemini CLI depends on ACP capabilities | PR #49449 (`acp: Enable history for external agents for all users`) |
| `docs/src/ai/tool-permissions.md` | Added new "Subcommand-Specific Patterns" section explaining how terminal permission patterns extract subcommands (e.g., `cargo build` vs `cargo test`) | PR #49148 (`Make terminal permission pattern suggestions subcommand-specific`) |
| `docs/src/configuring-languages.md` | Removed unnecessary blank line before Storage Location list | PR #49177 (`docs: Apply documentation standards`) |
| `docs/src/development.md` | Removed unnecessary blank lines in workflow steps | PR #49177 (`docs: Apply documentation standards`) |
| `docs/src/extensions/themes.md` | Removed unnecessary blank lines after numbered list items | PR #49177 (`docs: Apply documentation standards`) |
| `docs/src/languages/r.md` | Removed unnecessary blank line in extension list | PR #49177 (`docs: Apply documentation standards`) |
| `docs/src/reference/all-settings.md` | Removed unnecessary blank line before list in preview tabs description | PR #49177 (`docs: Apply documentation standards`) |
| `docs/src/vim.md` | Removed unnecessary blank line before list in text objects section | PR #49177 (`docs: Apply documentation standards`) |

### Rationale

These documentation updates fall into two categories:

1. **Feature documentation updates**: The external agents and tool permissions changes reflect actual code changes that modified user-facing behavior:
   - Thread history was enabled for external agents (Claude Agent, Codex) in PR #49449
   - Terminal permission patterns now extract subcommands for more granular control in PR #49148

2. **Formatting standardization**: Several files had inconsistent blank line usage around numbered lists with sub-items. These were normalized to follow consistent markdown formatting without unnecessary blank lines.

### Review Notes

- **Thread history wording**: The external-agents.md changes distinguish between agents that fully support thread history (Claude Agent, Codex) and Gemini CLI which depends on its ACP implementation. Reviewers should verify this distinction is accurate.
- **Subcommand patterns table**: The new section in tool-permissions.md includes a table showing example patterns. Verify the regex patterns (`^cargo\s+build\b`, etc.) match the actual implementation in the codebase.
- **Formatting changes**: The blank line removals are purely cosmetic and shouldn't affect rendered output—they simply align with the project's markdown standards.

Triggered by: pr 48999

Co-authored-by: factory-droid[bot] <138933559+factory-droid[bot]@users.noreply.github.com>