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258258| Your repo's `.mcp.json` MCP servers | Yes, in a session with one repository | Part of the clone, found from the session's working directory |
259259| Your repo's `.claude/rules/` | Yes | Part of the clone |
260260| Your repo's `.claude/skills/`, `.claude/agents/`, `.claude/commands/` | Yes | Part of the clone |
261| Plugins declared in `.claude/settings.json` | Yes | Installed at session start from the [marketplace](/docs/en/plugin-marketplaces) you declared. Requires network access to reach the marketplace source |
261| Plugins and marketplaces declared in your repo's `.claude/settings.json` | No | A cloud session doesn't install the plugins a repository turns on under [`enabledPlugins`](/docs/en/settings-reference#enabledplugins), including ones from the marketplaces it lists under [`extraKnownMarketplaces`](/docs/en/settings-reference#extraknownmarketplaces). Enable the plugin for your claude.ai account instead, so Claude Code loads it as a [synced plugin](/docs/en/plugins-reference#synced-plugins) |
262262| Your organization's [server-managed settings](/docs/en/server-managed-settings) | Yes | Fetched from Anthropic's servers when the session starts. See [Surface coverage](/docs/en/model-config#surface-coverage) for how `availableModels` is enforced in cloud sessions. Settings deployed to your device through MDM or managed settings files don't apply, because the session runs on an Anthropic-managed VM; in a [self-hosted environment](/docs/en/self-hosted-environments), sessions also read the managed settings file in the runner image, per [how Claude Code combines managed sources](/docs/en/managed-settings#how-claude-code-combines-managed-sources) |
263263| Your user `~/.claude/CLAUDE.md` | No | Lives on your machine, not in the repo |
264264| Your user `~/.claude/skills/`, `~/.claude/agents/`, `~/.claude/commands/` | No | Live on your machine, not in the repo. Commit them to the repo's `.claude/` directory instead. Cloud sessions automatically load skills you enable on claude.ai |
265| Plugins enabled only in your user settings | No | User-scoped `enabledPlugins` lives in `~/.claude/settings.json`. Declare them in the repo's `.claude/settings.json` instead, or enable them for your claude.ai account so Claude Code loads them as [synced plugins](/docs/en/plugins-reference#synced-plugins) |
265| Plugins enabled only in your user settings | No | User-scoped `enabledPlugins` lives in `~/.claude/settings.json` on your machine. Enable them for your claude.ai account instead, so Claude Code loads them as [synced plugins](/docs/en/plugins-reference#synced-plugins) |
266266| MCP servers you added with `claude mcp add` at the default local scope or the user scope | No | Those write to `~/.claude.json` on your machine, not the repo. Add the server with `claude mcp add --scope project`, which writes the repo's [`.mcp.json`](/docs/en/mcp#project-scope), and commit that file. A session with one repository loads it |
267267| Transport variables in your repo's `.claude/settings.json` `env` block, such as `NODE_EXTRA_CA_CERTS` and the [mTLS client certificate variables](/docs/en/network-config#mtls-authentication) | No | The hosting environment manages the session's API connection, so Claude Code ignores these keys and notes each ignored key in the session's debug log |
268268| API keys and tokens for services Claude calls | On Pro and Max plans, as [API credentials](#add-api-credentials) | You add the key once on the environment and the agent proxy attaches it to requests for the hosts you list. A key the agent proxy [can't attach](#requests-that-never-get-the-credential), or any key on a Team or Enterprise plan, stays in an environment variable |