Built-in Tools

AtomCode ships built-in tools for filesystem & shell, code graph, web, automation, and native AtomGit operations. The model picks tools per task — you almost never need to specify them by hand.

Filesystem & shell (9)

Tool	Purpose	Confirmation?
`read_file`	Read file content; supports line offset and range	No
`write_file`	Write a full file (overwrite)	Sensitive paths: yes
`edit_file`	String-match local edits; returns the edited context	Sensitive paths: yes
`search_replace`	Batch string replacements; good for multi-line / multi-site patterns	Sensitive paths: yes
`bash`	Run shell commands; destructive commands trigger the permission dialog	Destructive: yes
`grep`	Regex search with ripgrep semantics	No
`glob`	Filename glob matching (e.g. `src/*/.ts`)	No
`list_directory`	List directory contents	No
`change_dir`	Switch the agent's current working directory	No

Sensitive paths

Writes to paths like /etc, ~/.ssh, and shell rc files always trigger the permission dialog — "always allow" cannot skip them. Likewise, rm on source files always needs explicit confirmation.

Background long-running tasks

Pass run_in_background: true to bash and the command launches as a detached process and returns immediately with a PID and a log-file path; the process survives across conversation turns — ideal for dev servers, file watchers, and tunnels, without blocking the session.

Destructive-command guard

High-risk commands like rm -rf, dd, mkfs, and sudo, plus schema-destroying database migrations (e.g. migrate:fresh, db:reset), always force a permission prompt. This confirmation always fires — even a prior "always allow" on bash cannot skip it.

Code graph (8)

This is what sets AtomCode apart from generic agents. With the code-graph index, the model can pinpoint symbols, references, and call relationships without scanning the entire tree — especially valuable on large repos.

Tool	Purpose
`list_symbols`	List all symbols defined in a file or directory (functions, classes, constants, …)
`read_symbol`	Read a symbol's full definition surgically, without dragging the entire file into context
`find_references`	Find every location that references a symbol
`trace_callers`	Walk the caller chain of a function backwards
`trace_callees`	Expand a function's downstream calls
`trace_chain`	Search for a possible call chain between two symbols
`file_deps`	Analyse a file's imports / dependency graph
`blast_radius`	Estimate the files / symbols a change to a given symbol could affect

Typical scenarios

Pre-refactor risk assessment — "How big is the blast if I change formatDate's signature?" The model calls blast_radius + find_references.
Bug root-causing — "Why doesn't this button respond?" Start at the entry function and trace_callees downward.
Understanding unfamiliar code — "Walk me through AuthService.login" → read_symbol + trace_callees.

Web (2)

Tool	Purpose
`web_search`	Search the web for keywords; returns a list of title / snippet / URL
`web_fetch`	Fetch a URL and convert it to markdown for the model

Typical uses: looking up the latest docs, comparing library APIs, reading a GitHub issue. In offline environments or to save cost, disable them with --disable-tools web_search,web_fetch.

Automation (2)

Tool	Purpose
`auto_fix`	Run the project's lint / typecheck and iterate over the error list until clean
`use_skill`	Invoke a user-defined skill — package a multi-step flow as a reusable command

See Skills for details.

AtomGit integration (3)

After /login, the model can operate AtomGit directly through these built-in tools. Describe the outcome in natural language; there is no /issue slash command.

Tool	Purpose	Confirmation?
`atomgit_repo`	List, inspect, create, delete, fork, or clone repositories; create tags and manage project labels	Writes: yes
`atomgit_pr`	List, inspect, create, close, and comment on pull requests; link or unlink related Issues	Writes: yes
`atomgit_issue`	List or inspect Issues; create an Issue and view, add, edit, or delete comments	Writes: yes

Ask: Create an AtomGit issue for this bug, including the reproduction steps and environment.

Large tool outputs

When a tool result is too large, AtomCode shows a stable preview and stores the full content with the current session. The model can page through the remainder with fetch_output, so “output truncated” does not mean the result was lost. Stored output is removed when its session is deleted.

Disabling specific tools

Use the --disable-tools flag at launch to hide tools from the model entirely. For example, inside the SWE-bench sandbox:

atomcode -p "solve this issue" --disable-tools web_search,web_fetch

Disabled tools don't appear in the tool schemas, so the model won't attempt to call a tool guaranteed to fail.

Next steps

Sessions & Undo — every file-edit tool routes through file-history, so /undo can roll back changes
Skills — wrap your own workflows with use_skill