Deep Agents Code stores data in two directory hierarchies:
~/.deepagents/ — Deep Agents-specific data (agent memory, skills, sessions)~/.agents/ — Tool-agnostic data (skills shared across AI CLI tools)
Directory structure
~/.deepagents/
├── .state/ # Per-machine Deep Agents Code state (managed automatically)
│ ├── sessions.db # SQLite database for conversation checkpoints
│ ├── history.jsonl # Command input history
│ ├── ... # Other markers & credentials
└── {agent}/ # Per-agent directory (default: "agent")
├── AGENTS.md # User customizations to agent instructions
├── skills/ # User-level skills
│ └── {skill-name}/
│ └── SKILL.md
└── agents/ # Custom subagent definitions
└── {subagent-name}/
└── AGENTS.md
~/.agents/ # Tool-agnostic alias (shared across AI CLIs)
└── skills/ # Skills available to any compatible tool
└── {skill-name}/
└── SKILL.md
{project}/ # Project-level (in git repo root)
├── AGENTS.md # Project instructions (root-level)
└── .deepagents/
│ ├── AGENTS.md # Project instructions (preferred location)
│ ├── skills/ # Project-specific skills
│ │ └── {skill-name}/
│ │ └── SKILL.md
│ └── agents/ # Project-specific subagents
│ └── {subagent-name}/
│ └── AGENTS.md
└── .agents/ # Tool-agnostic project skills
└── skills/
└── {skill-name}/
└── SKILL.md
What goes where
| Data | Location | Read/Write | Notes |
|---|
| Sessions | ~/.deepagents/.state/sessions.db | R/W | SQLite checkpoint database |
| Input history | ~/.deepagents/.state/history.jsonl | R/W | JSON-lines, up/down arrow recall |
| Base instructions | Package default_agent_prompt.md | R | Immutable, updated with Deep Agents Code upgrades |
| User customizations | ~/.deepagents/{agent}/AGENTS.md | R/W | Appended to base instructions |
| Project instructions | .deepagents/AGENTS.md or AGENTS.md | R | Both loaded if present |
| User skills | ~/.deepagents/{agent}/skills/ | R/W | Agent-specific skills |
| Shared skills | ~/.agents/skills/ | R | Tool-agnostic, cross-CLI |
| Project skills | .deepagents/skills/ or .agents/skills/ | R | Project-scoped |
| Custom subagents | ~/.deepagents/{agent}/agents/ | R/W | User-defined subagents |
| Project subagents | .deepagents/agents/ | R | Project-defined subagents |
Precedence rules
When the same item exists in multiple locations, higher precedence wins completely (no merging).
Skills
Precedence order (lowest to highest):
~/.deepagents/{agent}/skills/ — User Deep Agents Code~/.agents/skills/ — User tool-agnostic.deepagents/skills/ — Project Deep Agents Code.agents/skills/ — Project tool-agnostic (highest)
When a skill is loaded, Deep Agents Code verifies that the resolved file path stays within one of these directories. Symlinks that resolve outside all skill roots are rejected. To allow symlink targets in additional directories, see [skills].extra_allowed_dirs.
Subagents
Precedence order (lowest to highest):
~/.deepagents/{agent}/agents/ — User-level.deepagents/agents/ — Project-level (highest)
Each subagent is an AGENTS.md file with YAML frontmatter (name, description, optional model) and a markdown body for the system prompt. See Use subagents in Deep Agents Code for the full format reference.
Instructions
All instruction sources are combined (not overridden):
- Package base prompt (always loaded)
~/.deepagents/{agent}/AGENTS.md (appended).deepagents/AGENTS.md (appended)AGENTS.md at project root (appended)
.deepagents vs .agents
| Directory | Purpose | When to use |
|---|
.deepagents/ | Deep Agents Code-specific | Skills and config that use Deep Agents Code-specific features |
.agents/ | Tool-agnostic | Skills you want to share across different AI CLI tools |
Use .agents/skills/ for skills that work with any AI coding assistant.
Use .deepagents/skills/ for skills that rely on Deep Agents-specific tools or conventions.
Cleaning up
| Need | Action |
|---|
| Reset all data | rm -rf ~/.deepagents |
| Clear sessions only | rm ~/.deepagents/.state/sessions.db* |
| Clear input history | rm ~/.deepagents/.state/history.jsonl |
| Clear stored API keys | rm ~/.deepagents/.state/auth.json |
| Clear MCP OAuth tokens | rm -rf ~/.deepagents/.state/mcp-tokens |
| Clear MCP project trust | rm ~/.deepagents/.state/mcp_trust.json |
| Re-run first-run onboarding | rm ~/.deepagents/.state/onboarding_complete |
| Reset agent instructions | dcode agents reset --agent {name} |
| Remove a skill | rm -rf ~/.deepagents/{agent}/skills/{skill-name} |
Deleting ~/.deepagents/.state/sessions.db will remove all conversation history and checkpoints.This cannot be undone unless you have a backup of the sessions.db file.
