Atlas plans a multi-file JavaScript change before a single line is edited by putting you in a plan agent whose description is literally Plan mode. Disallows all edit tools. The plan agent's permission set denies edit for every path except the plan markdown under .atlas/plans/*.md, so research with codebase_search, grep, read, and the lsp tool cannot turn into an edit of a .js file. You map the module graph around package.json, name the vitest specs at risk, then call plan_exit to hand off to the build agent.
How do you design a multi-file JavaScript change before touching the code?
Atlas designs a multi-file JavaScript change inside a plan agent described as Plan mode. Disallows all edit tools. The permission set denies edit for "*" and allows it only under .atlas/plans/*.md, so mapping a module graph around package.json in 2026 cannot modify a .js file by accident.
The job to be done is designing a change that touches many files, and getting it reviewed, before a single line is modified. In JavaScript the classic case is a rename that must travel through index.js re-export barrels, an npm script rename in package.json, or a bundler config change that shifts an entry point. Atlas drafts a plan in a read-only plan agent and asks before switching to a build agent. Every Atlas tool call is permission-gated against allow, ask, and deny rules before it runs, so plan mode is a guarantee, not a promise the model makes to itself.
Which Atlas tools work in JavaScript plan mode?
Atlas leaves 6 tools switched on in plan mode: plan_exit, codebase_search, grep, read, lsp, and question. Research with codebase_search, grep, read, and the lsp tool all stay allowed, so you can enumerate every callsite of a JavaScript function before deciding how its signature should change.
Planning a JavaScript change is mostly a measuring exercise. codebase_search finds the modules that implement the behavior even when your wording never appears in the source, because Atlas indexes code by AST declarations using tree-sitter. grep confirms literal occurrences across your .js sources and the scripts block in package.json, catching the places a rename would break the build. The lsp tool's callsite operations see through the re-export barrels that make JavaScript blast radius hard to eyeball. The question tool lets Atlas ask instead of assume while the design is still open.
Where does Atlas write the plan file in a JavaScript repo?
Atlas writes the plan into a markdown file under .atlas/plans/, the only path plan mode is permitted to write in 2026. The plan agent's permission set denies edit for "*" and allows only .atlas/plans/*.md, so your .js modules, package.json, and vitest specs stay read-only while the design is drafted.
Keeping the plan in the repository makes it reviewable exactly like code, on a branch and in a diff, before anyone writes an edit. The plan file sits next to your working tree under .atlas/plans/, so it is reviewed on the branch rather than in a chat log you lose. A strong JavaScript plan names the modules to touch, the index.js barrels that must be updated, the npm scripts affected in package.json, which vitest specs must change, and whether prettier will reflow any file that the change is about to modify.
How does plan_exit switch Atlas from planning to building?
Atlas leaves plan mode through the plan_exit tool, which asks 1 question: Plan at <path> is complete. Would you like to switch to the build agent and start implementing? Answering Yes hands off to the build agent. Answering No raises Question.RejectedError and keeps you refining the JavaScript plan.
The handoff is an explicit gate rather than a silent transition, which is why Atlas separates the plan agent from the build agent at all. Until you answer Yes, no .js file can be edited, because the plan agent denies edit for every path other than the plan markdown. After you answer Yes, the build agent implements the plan, and every edit to a .js module arrives as a diff you approve before vitest runs. Answering No is an ordinary outcome: Question.RejectedError returns you to planning with all of your research context intact.
How do you verify a planned JavaScript change with pnpm, vitest, and prettier?
Atlas verifies a planned JavaScript change after the plan_exit handoff with the project's 3 real commands. Install with pnpm, run vitest to prove the specs the plan flagged as at-risk still pass, and run prettier so the diff you review shows logic changes rather than reflowed lines.
A plan is only as strong as its test story, so the markdown written under .atlas/plans/ should name which vitest specs must change and which must keep passing untouched. Once the build agent starts implementing, vitest is the arbiter, and pnpm keeps the install reproducible against the lockfile so the result is not an artifact of a stale node_modules tree. Running prettier before review keeps a multi-file JavaScript diff readable. pnpm keeps the install reproducible, so a failing vitest run after the handoff means the plan was wrong and not a stale node_modules tree.
What belongs in an Atlas plan file for a JavaScript change?
An Atlas plan file for a JavaScript change names 5 things: the .js modules to touch, the index.js barrels to update, the npm scripts in package.json affected, the vitest specs at risk, and whether prettier will reflow a file. The plan lives under .atlas/plans/.
A JavaScript plan that names its index.js barrels survives contact with the module graph, because a rename that stops at the implementation file breaks every consumer importing through the barrel. A plan that names the npm scripts in package.json catches the build breaking before the build breaks. A plan that names the vitest specs gives the build agent a definition of done. Writing all of that into the plan markdown under .atlas/plans/ before calling plan_exit is what turns a later pnpm install and vitest run into a real check rather than a hope.
How do you size a JavaScript refactor before you start editing?
Sizing a JavaScript refactor means counting 3 things while the Atlas plan agent still denies edit: the .js modules that import the symbol, the index.js barrels that re-export it, and the vitest specs that mock it. grep and the lsp tool produce all 3 lists without writing a byte.
A JavaScript rename escapes its module immediately, because an index.js barrel can re-export the symbol under a different name and a consumer three packages away imports that name instead. grep through ripgrep lists the literal occurrences across your .js sources and the scripts block in package.json. The lsp tool lists the callsites text search misses. vitest specs that mock the symbol are the definition of done, and pnpm decides which workspace packages are even in scope. All of it belongs in the plan markdown before plan_exit hands the work to the build agent.
Step by step
- 01Switch to the Atlas plan agent; its permissions deny edit for "*" and allow it only under .atlas/plans/*.md, so your .js files and package.json are read-only.
- 02Research the blast radius with codebase_search, grep, read, and the lsp tool; all four stay allowed in plan mode.
- 03Use grep with include filters across your .js sources to list every index.js barrel and vitest spec the change will break.
- 04Write the plan into the allowed markdown path under .atlas/plans/, naming the modules to touch, the npm scripts in package.json to update, and the bundler config implications.
- 05Call plan_exit: it asks Plan at <path> is complete. Would you like to switch to the build agent and start implementing?
- 06Answer Yes to hand off to the build agent, or answer No to raise Question.RejectedError and keep refining the JavaScript plan.
- 07After the build agent implements, install with pnpm and run vitest to prove the specs the plan named still pass.
- 08Run prettier, then review the unified diff Atlas surfaces for every file edit before it writes.
Frequently asked questions
- how do I get an AI agent to plan a JavaScript refactor before it edits anything
- Switch to the Atlas plan agent. Its permission set denies edit for "*" and allows writing only under .atlas/plans/*.md, so research with codebase_search, grep, read, and the lsp tool cannot modify a .js file.
- how do I find every file a JavaScript rename will break
- Inside Atlas plan mode, enumerate callsites with the lsp tool and confirm with grep across your .js sources and the scripts block in package.json. Both tools stay allowed while edit is denied for every source path.
- what does plan_exit do in Atlas
- plan_exit ends plan mode. It asks Plan at <path> is complete. Would you like to switch to the build agent and start implementing? Yes hands off to the build agent, and No raises Question.RejectedError so you keep planning.
- where does Atlas store the plan for a JavaScript change
- Atlas writes the plan into a markdown file under .atlas/plans/, the only path plan mode can write. Your .js modules, package.json, and bundler config stay read-only until you exit plan mode.
- can an AI agent accidentally edit code while researching a JavaScript change
- Not in Atlas plan mode. The plan agent's permission set denies edit for "*", and every Atlas tool call is permission-gated against allow, ask, and deny rules before it runs.
- how do I make sure a multi-file JavaScript change does not break vitest
- Name the at-risk vitest specs in the plan file before the plan_exit handoff, then install with pnpm and run vitest once the build agent has implemented. prettier keeps the diff readable while you review.
- can I roll back an AI agent's JavaScript edits
- Yes. Atlas snapshots file changes as git patches so edits can be diffed and rolled back, and it computes a unified diff for every file edit and surfaces it for approval before writing.
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