1> ## Documentation Index

2> Fetch the complete documentation index at: https://code.claude.com/docs/llms.txt

3> Use this file to discover all available pages before exploring further.

4 

5# Explore the .claude directory

6 

7> Where Claude Code reads CLAUDE.md, settings.json, hooks, skills, commands, subagents, workflows, rules, and auto memory. Explore the .claude directory in your project and ~/.claude in your home directory.

8 

9Claude Code reads instructions, settings, skills, subagents, and memory from your project directory and from `~/.claude` in your home directory. Commit project files to git to share them with your team; files in `~/.claude` are personal configuration that applies across all your projects.

10 

11On Windows, `~/.claude` resolves to `%USERPROFILE%\.claude`. If you set [`CLAUDE_CONFIG_DIR`](/en/env-vars), every `~/.claude` path on this page lives under that directory instead.

12 

13Most users only edit `CLAUDE.md` and `settings.json`. The rest of the directory is optional: add skills, rules, or subagents as you need them.

14 

15## Explore the directory

16 

17Click files in the tree to see what each one does, when it loads, and an example.

18 

19## What's not shown

20 

21The explorer covers files you author and edit. A few related files live elsewhere:

22 

23| File | Location | Purpose |

24| ----------------------- | -------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |

25| `managed-settings.json` | System-level, varies by OS | Enterprise-enforced settings that you can't override. See [server-managed settings](/en/server-managed-settings). |

26| `CLAUDE.local.md` | Project root | Your private preferences for this project, loaded alongside CLAUDE.md. Create it manually and add it to `.gitignore`. |

27| Installed plugins | `~/.claude/plugins` | Cloned marketplaces, installed plugin versions, and per-plugin data, managed by `claude plugin` commands. Orphaned versions are deleted 7 days after a plugin update or uninstall. See [plugin caching](/en/plugins-reference#plugin-caching-and-file-resolution). |

28 

29`~/.claude` also holds data Claude Code writes as you work: transcripts, prompt history, file snapshots, caches, and logs. See [application data](#application-data) below.

30 

31## Choose the right file

32 

33Different kinds of customization live in different files. Use this table to find where a change belongs.

34 

35| You want to | Edit | Scope | Reference |

36| :------------------------------------------------- | :--------------------------------------- | :---------------- | :------------------------------------------------- |

37| Give Claude project context and conventions | `CLAUDE.md` | project or global | [Memory](/en/memory) |

38| Allow or block specific tool calls | `settings.json` `permissions` or `hooks` | project or global | [Permissions](/en/permissions), [Hooks](/en/hooks) |

39| Run a script before or after tool calls | `settings.json` `hooks` | project or global | [Hooks](/en/hooks) |

40| Set environment variables for the session | `settings.json` `env` | project or global | [Settings](/en/settings#available-settings) |

41| Keep personal overrides out of git | `settings.local.json` | project only | [Settings scopes](/en/settings#settings-files) |

42| Add a prompt or capability you invoke with `/name` | `skills/<name>/SKILL.md` | project or global | [Skills](/en/skills) |

43| Define a specialized subagent with its own tools | `agents/*.md` | project or global | [Subagents](/en/sub-agents) |

44| Orchestrate many subagents from a script | `workflows/*.js` | project or global | [Dynamic workflows](/en/workflows) |

45| Connect external tools over MCP | `.mcp.json` | project only | [MCP](/en/mcp) |

46| Change how Claude formats responses | `output-styles/*.md` | project or global | [Output styles](/en/output-styles) |

47 

48## File reference

49 

50This table lists every file the explorer covers. Project-scope files live in your repo under `.claude/` (or at the root for `CLAUDE.md`, `.mcp.json`, and `.worktreeinclude`). Global-scope files live in `~/.claude/` and apply across all projects.

51 

52<Note>

53 Several things can override what you put in these files:

54 

55 * [Managed settings](/en/server-managed-settings) deployed by your organization take precedence over everything

56 * CLI flags like `--permission-mode` or `--settings` override `settings.json` for that session

57 * Some environment variables take precedence over their equivalent setting, but this varies: check the [environment variables reference](/en/env-vars) for each one

58 

59 See [settings precedence](/en/settings#settings-precedence) for the full order.

60</Note>

61 

62Click a filename to open that node in the explorer above.

63 

64| File | Scope | Commit | What it does | Reference |

65| --------------------------------------------------- | ------------------ | ------ | ------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------- |

66| [`CLAUDE.md`](#ce-claude-md) | Project and global | ✓ | Instructions loaded every session | [Memory](/en/memory) |

67| [`rules/*.md`](#ce-rules) | Project and global | ✓ | Topic-scoped instructions, optionally path-gated | [Rules](/en/memory#organize-rules-with-claude/rules/) |

68| [`settings.json`](#ce-settings-json) | Project and global | ✓ | Permissions, hooks, env vars, model defaults | [Settings](/en/settings) |

69| [`settings.local.json`](#ce-settings-local-json) | Project only | | Your personal overrides, gitignored when Claude Code creates it | [Settings scopes](/en/settings#settings-files) |

70| [`.mcp.json`](#ce-mcp-json) | Project only | ✓ | Team-shared MCP servers | [MCP scopes](/en/mcp#mcp-installation-scopes) |

71| [`.worktreeinclude`](#ce-worktreeinclude) | Project only | ✓ | Gitignored files to copy into new worktrees | [Worktrees](/en/worktrees#copy-gitignored-files-into-worktrees) |

72| [`skills/<name>/SKILL.md`](#ce-skills) | Project and global | ✓ | Reusable prompts invoked with `/name` or auto-invoked | [Skills](/en/skills) |

73| [`commands/*.md`](#ce-commands) | Project and global | ✓ | Single-file prompts; same mechanism as skills | [Skills](/en/skills) |

74| [`output-styles/*.md`](#ce-output-styles) | Project and global | ✓ | Custom system-prompt sections | [Output styles](/en/output-styles) |

75| [`agents/*.md`](#ce-agents) | Project and global | ✓ | Subagent definitions with their own prompt and tools | [Subagents](/en/sub-agents) |

76| [`workflows/*.js`](#ce-workflows) | Project and global | ✓ | Dynamic workflow scripts written by Claude and saved from `/workflows`; each file becomes a `/<name>` command | [Dynamic workflows](/en/workflows) |

77| [`agent-memory/<name>/`](#ce-agent-memory) | Project and global | ✓ | Persistent memory for subagents | [Persistent memory](/en/sub-agents#enable-persistent-memory) |

78| [`~/.claude.json`](#ce-claude-json) | Global only | | App state, OAuth, UI toggles, personal MCP servers | [Global config](/en/settings#global-config-settings) |

79| [`projects/<project>/memory/`](#ce-global-projects) | Global only | | Auto memory: Claude's notes to itself across sessions | [Auto memory](/en/memory#auto-memory) |

80| [`keybindings.json`](#ce-keybindings) | Global only | | Custom keyboard shortcuts | [Keybindings](/en/keybindings) |

81| [`themes/*.json`](#ce-themes) | Global only | | Custom color themes | [Custom themes](/en/terminal-config#create-a-custom-theme) |

82 

83## Troubleshoot configuration

84 

85If a setting, hook, or file isn't taking effect, see [Debug your configuration](/en/debug-your-config) for the inspection commands and a symptom-first lookup table.

86 

87## Application data

88 

89Beyond the config you author, `~/.claude` holds data Claude Code writes during sessions. These files are plaintext. Anything that passes through a tool lands in a transcript on disk: file contents, command output, pasted text.

90 

91### Cleaned up automatically

92 

93Files in the paths below are deleted on startup once they're older than [`cleanupPeriodDays`](/en/settings#available-settings). The default is 30 days.

94 

95| Path under `~/.claude/` | Contents |

96| -------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------- |

97| `projects/<project>/<session>.jsonl` | Full conversation transcript: every message, tool call, and tool result |

98| `projects/<project>/<session>/subagents/` | [Subagent](/en/sub-agents) conversation transcripts, removed with the parent session transcript when it ages out |

99| `projects/<project>/<session>/tool-results/` | Large tool outputs spilled to separate files |

100| `file-history/<session>/` | Pre-edit snapshots of files Claude changed, used for [checkpoint restore](/en/checkpointing) |

101| `plans/` | Plan files written during [plan mode](/en/permission-modes#analyze-before-you-edit-with-plan-mode) |

102| `debug/` | Per-session debug logs, written only when you start with `--debug` or run `/debug` |

103| `paste-cache/`, `image-cache/` | Contents of large pastes and attached images |

104| `session-env/` | Per-session environment metadata |

105| `tasks/` | Per-session task lists written by the task tools |

106| `shell-snapshots/` | Captured shell environment used by the Bash tool. Removed on clean exit. The sweep clears any left after a crash. |

107| `backups/` | Timestamped copies of `~/.claude.json` taken before config migrations |

108| `feedback-bundles/` | Redacted transcript archives written by `/feedback` on third-party providers, for sending to your Anthropic account team |

109| `todos/`, `statsig/`, `logs/` | Legacy directories from older versions. No longer written. The sweep removes their contents and then the empty directory. |

110 

111### Kept until you delete them

112 

113The following paths are not covered by automatic cleanup and persist indefinitely.

114 

115| Path under `~/.claude/` | Contents |

116| ----------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |

117| `history.jsonl` | Every prompt you've typed, with timestamp and project path. Used for up-arrow recall. |

118| `stats-cache.json` | Aggregated token and cost counts shown by `/usage` |

119| `remote-settings.json` | Cached copy of [server-managed settings](/en/server-managed-settings) for your organization. Only present when your organization has configured them. Refreshed on each launch. |

120 

121Other small cache and lock files appear depending on which features you use and are safe to delete.

122 

123### Plaintext storage

124 

125Transcripts and history are not encrypted at rest. OS file permissions are the only protection. If a tool reads a `.env` file or a command prints a credential, that value is written to `projects/<project>/<session>.jsonl`. To reduce exposure:

126 

127* Lower `cleanupPeriodDays` to shorten how long transcripts are kept

128* Set the [`CLAUDE_CODE_SKIP_PROMPT_HISTORY`](/en/env-vars) environment variable to skip writing transcripts and prompt history in any mode. In non-interactive mode, you can instead pass `--no-session-persistence` alongside `-p`, or set `persistSession: false` in the Agent SDK.

129* Use [permission rules](/en/permissions) to deny reads of credential files

130 

131### Clear local data

132 

133Run `claude project purge` to delete the state Claude Code holds for one project. The command requires Claude Code v2.1.124 or later. It deletes:

134 

135* Transcripts and auto memory under `projects/`

136* Per-session `tasks/`, `debug/`, and `file-history/` entries

137* Matching prompt lines in `history.jsonl`

138* The project's entry in `~/.claude.json`

139 

140The command prints the full deletion plan and asks for confirmation before removing anything.

141 

142Preview the plan without deleting anything:

143 

144```bash theme={null}

145claude project purge ~/work/my-repo --dry-run

146```

147 

148Delete with a single confirmation prompt:

149 

150```bash theme={null}

151claude project purge ~/work/my-repo

152```

153 

154Omit the path to pick a project from an interactive list.

155 

156Skip the confirmation prompt for use in scripts:

157 

158```bash theme={null}

159claude project purge ~/work/my-repo --yes

160```

161 

162Pass `--all` instead of a path to purge state for every project at once, which deletes `history.jsonl` outright rather than filtering it. Pass `-i` to step through the deletion plan one item at a time.

163 

164The command leaves `shell-snapshots/` and `backups/` alone because those are not project-scoped, and warns about them in the plan output. It exits with status 1 if no state matches the given path.

165 

166You can also delete any of the application-data paths above by hand. New sessions are unaffected. The table below shows what you lose for past sessions.

167 

168| Delete | You lose |

169| -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------ |

170| `~/.claude/projects/` | Resume, continue, and rewind for past sessions |

171| `~/.claude/history.jsonl` | Up-arrow prompt recall |

172| `~/.claude/file-history/` | Checkpoint restore for past sessions |

173| `~/.claude/stats-cache.json` | Historical totals shown by `/usage` |

174| `~/.claude/remote-settings.json` | Nothing. Re-fetched on next launch. |

175| `~/.claude/debug/`, `~/.claude/plans/`, `~/.claude/paste-cache/`, `~/.claude/image-cache/`, `~/.claude/session-env/`, `~/.claude/tasks/`, `~/.claude/shell-snapshots/`, `~/.claude/backups/` | Nothing user-facing |

176| `~/.claude/todos/`, `~/.claude/statsig/`, `~/.claude/logs/` | Nothing. Legacy directories not written by current versions. |

177 

178Don't delete `~/.claude.json`, `~/.claude/settings.json`, or `~/.claude/plugins/`: those hold your auth, preferences, and installed plugins.

179 

180## Related resources

181 

182* [Manage Claude's memory](/en/memory): write and organize CLAUDE.md, rules, and auto memory

183* [Configure settings](/en/settings): set permissions, hooks, environment variables, and model defaults

184* [Create skills](/en/skills): build reusable prompts and workflows

185* [Configure subagents](/en/sub-agents): define specialized agents with their own context