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Bash Command Restrictions: A configurable allow/deny engine that gates every bash command the agent runs. Trusted patterns run automatically, denied patterns always prompt, and everything else requires explicit approval. See BASH_COMMAND_RESTRICTIONS.md for configuration details, pattern syntax, and edge cases.
Configurable Permission Timeout: Permission dialogs auto-deny after a configurable timeout (default: 5 minutes). Set to 0 for infinite wait. Configurable in Settings → Bash Commands.
Customizable System Prompt: The AI's system prompt is fully editable via Settings → System Prompt. Each section (identity, behavioral rules, citations, tool routing) is a separate file that can be independently edited, disabled, or reset. Workspace-level overrides in .cowork/prompts/ replace global sections per-project. Template variables ({{cwd}}, {{project_name}}, {{date}}, {{model}}) are resolved at runtime.
Per-Session MCP Server Toggle: Disable/enable MCP servers on-the-fly from the Context Panel without restarting the session. Reduces context window token usage by shedding unused tool schemas mid-conversation. Supports workspace-level profiles via .cowork/mcp-servers.json (committable to git) for team-wide defaults.
Skill Pinning: Star/pin specific skills (semantic-index, firecrawl, docx, etc.) to explicitly tell the AI to prioritize them for the current session. All skills remain available — pinning adds emphasis, not restriction. Select skills on the Welcome screen before starting a chat, or pin/unpin mid-conversation from the Context Panel. Enforces a max of 10 pinned skills per session with full validation.
Skill Workspace Profiles: Disable unused skills per-session to reduce context window usage. Three-layer resolution: Session > Workspace profile (.cowork/skills-profile.json) > Global config. Welcome page loads the workspace profile automatically and shows three skill states (★ Pinned, ☆ Available, ✕ Removed). Context Panel supports mid-conversation remove/restore with a 💾 save button to persist changes. New sessions immediately respect the workspace profile.
Skill Conflict Resolution: Policy engine for resolving name collisions between custom and built-in skills. Three policies: custom-wins (recommended), builtin-wins, or ask (notification + manual choice). Per-skill source overrides, global disable toggles, conflict count badge in Settings sidebar, and toast notifications on new conflicts. Managed via Settings → Skills.Bash