Copilot CLI config files and locations

Directory where the CLI stores configuration, session history, logs, and customizations. Relocate with COPILOT_HOME.

Primary user configuration file (JSONC) with global defaults for all repositories. Invalid or unknown keys are listed in the /settings Problems tab; symlinked files are written through.

Automatically managed application state (authentication, installed plugins, trusted folders). User settings left here are ignored.

Personal custom instructions applied to all sessions.

Additional personal *.instructions.md files loaded alongside copilot-instructions.md for all sessions.

User-level MCP server definitions (mcpServers key), available in all sessions; lowest priority among MCP sources.

User-level LSP server definitions under an lspServers key; manage with /lsp or edit directly.

User-level BYOK provider and model registry with providers and models keys; overridden in location by COPILOT_PROVIDERS_CONFIG.

Personal custom agent definitions (.agent.md files); highest priority custom agent location.

Personal skills, each in a subdirectory with a SKILL.md file; project skills of the same name take precedence.

User-level hook configuration *.json files applied to all sessions ($COPILOT_HOME/hooks/ when set).

User-level extension files available across sessions.

Saved tool and directory approvals keyed by absolute location path (locations.<key>.tool_approvals and allowed_directories). Does not support deny, ask, or URL rules.

Session history by session ID (events.jsonl plus plans, checkpoints, tracked files); enables --resume and --continue.

Command history used for Ctrl+R reverse search and history navigation; managed automatically.

SQLite database for cross-session data such as checkpoint indexing and search; rebuild with /chronicle reindex.

Session log files named process-{timestamp}-{pid}.log, plus extension logs under logs/extensions/.

Installed plugin files: installed-plugins/{marketplace-name}/{plugin-name}/ for marketplace installs and installed-plugins/_direct/ for direct installs.

Persistent data for installed plugins, managed by the plugins themselves.

Lock files and state for IDE integrations; managed automatically.

MCP OAuth token, registration, and PKCE fallback files when keychain storage is unavailable.

Fallback storage and index for MCP secret placeholders when keychain storage is unavailable.

Repository settings committed and shared with collaborators; only a fixed set of keys is supported, each with a fail-closed merge policy.

Personal repository overrides that should not be committed (add to .gitignore); same schema as repository settings and takes precedence over them.

Read (with .claude/settings.local.json) for the shared cross-tool subset of repository settings, such as companyAnnouncements, disableAllHooks, enabledPlugins, extraKnownMarketplaces, and hooks.

Plain-text allowlist restricting which built-in models a repository can use: glob lines, # comments, and exactly one fallback: MODEL-ID. Does not filter BYOK models.

Workspace MCP server configuration loaded from the working directory up to the Git root when the folder is trusted. Migrate from .vscode/mcp.json by remapping servers to mcpServers.

Repository MCP server configuration (medium trust), loaded like .mcp.json for trusted folders.

Project LSP server configuration applying to everyone in the repository; can disable a server with "disabled": true.

Repository-level hook configuration files (JSON, version 1).

Machine-wide policy hooks (Windows: C:\ProgramData\GitHub\Copilot\policy.d\*.json or HKLM\Software\Policies\GitHub\Copilot). Load first and cannot be disabled by disableAllHooks.

File-based MDM managed settings: /etc/github-copilot/managed-settings.json (Linux), /Library/Application Support/GitHubCopilot/managed-settings.json (macOS), %ProgramFiles%\GitHubCopilot\managed-settings.json (Windows). Rejected on POSIX if a symlink, not root-owned, or world-writable.

macOS MDM plist domain for managed settings.

Windows MDM registry location for managed settings.

Repository custom instructions read from the Git root and cwd; created or updated by copilot init and /init. Supports @path imports.

Custom instructions file read from the Git root and cwd; supports @path imports.

Custom instructions file read from the Git root and cwd; supports @path imports.

Custom instructions file read from the Git root and cwd.

Path-scoped instruction files read from the Git root and cwd; scope with paths or applyTo frontmatter.

Claude Code rule files read like .github/instructions files; scope with paths (or applyTo) frontmatter.

Project skills location (highest priority), also inherited from parent directories in monorepos.

Alternative project skills location.

Claude-compatible project skills location.

Personal agent skills shared across all projects.

Project custom agents, loaded from the cwd upward to the Git root (priority 2).

Project custom agents, loaded from the cwd upward to the Git root after all .github/agents/ directories (priority 3).

Commands stored as individual .md files, an alternative skill format named after the file; lower priority than same-named skills.

Plugin manifest. Agent Plugins plugins use plugin.json at the root; legacy plugins check .plugin/plugin.json, plugin.json, .github/plugin/plugin.json, .claude-plugin/plugin.json in order.

Plugin marketplace manifest, checked as marketplace.json, .plugin/marketplace.json, .github/plugin/marketplace.json, .claude-plugin/marketplace.json in order; requires name, owner, plugins.