# how to run coding agents in parallel without conflicts

2026-09-30, updated 2026-09-30

By Jawad Jalal. Founder of Wayari. Builds the desktop app and its coding-agent workflow.

separate worktrees protect files. clear ownership protects the change. decide where agents can work together before they start editing the same seam.


To run coding agents in parallel, give each one a separate worktree and a bounded part of the job. Agree on shared interfaces before both sides start changing them. Check the combined result before merging.

Separate directories solve the collision where two agents overwrite the same local file. They cannot solve two different answers to the same design question.

That second collision often arrives at integration, when both branches look reasonable on their own.

## what does a separate worktree protect?

A Git worktree gives a branch its own working directory. One agent can edit and test there while another works elsewhere.

They share the repository's history. They do not share the same uncommitted files.

The [Git worktree manual](https://git-scm.com/docs/git-worktree) describes that relationship. Wayari gives agents their own branches and worktrees; the [branches documentation](/docs#branches) explains how those fit inside a job.

This matters even for a small task. An agent that runs a formatter or switches a branch in a shared checkout can change what the other agent is reading halfway through its work.

## how should you divide the job?

Suppose a job adds CSV export to a report page. One builder could handle the export function and its tests. Another could handle the button and its loading state.

Before they start, agree on what the function takes, what it returns and who owns the file that declares it.

If both builders invent that interface, integration becomes a second implementation pass.

Write the boundary in the tasks. "Own the export module; keep the agreed signature" is more useful than "work on the backend" in a repository where the frontend and backend import the same types.

## what if both agents need the same file?

Lockfiles, route registries and common types attract changes from unrelated work. Two agents can have separate tasks and still meet in those files.

Let one builder own the shared edit. Give the other builder the interface it needs, or make its work depend on that edit landing first.

When discovery changes the boundary, update the plan. A claim made before editing is cheaper than a conflict found after both agents finish.

The [integration documentation](/docs#integration) describes Wayari's integration step. Treat a conflict as information about the split, rather than a reason to let one builder silently discard the other's work.

## when should agents work in sequence?

Parallel work is useful when the pieces can be built independently. A schema change and code that depends on the final schema usually need an order.

The same applies when a refactor moves the files another agent is about to edit. Finish the move, then start the dependent change from that result.

Running both at once makes the activity graph look busy. It can make the usable change arrive later.

## which branch should you test?

The export builder's tests can pass. The button builder's tests can pass. The button can still call the export function with the wrong arguments after integration.

Run the checks at the combined head. Open the report and export a real file from it. Read that file.

The [gate](/blog/loop-until-it-holds) records what ran. The [independent reviewer](/blog/the-reviewer-is-never-the-author) reads what the builders put together.

## should this task run in parallel?

Choose the order from the dependency, then assign the builder.

| Work | Useful order | Check after integration |
| --- | --- | --- |
| Export function and report button, with an agreed signature | Separate worktrees can run together. | Export a file through the button and inspect it. |
| Schema migration and callers of the new schema | Settle the schema before changing the callers. | Run migration and caller checks on the combined head. |
| File move and edits to those files | Finish the move first. | Confirm imports and behaviour after the edits. |

## how many agents should a job have?

Use as many as the job has independent pieces you can describe. A typo usually has one. An export feature may have several. A change to a central interface may need one builder and a reviewer.

Every additional builder creates another result somebody must integrate. Measure the finished pull request, including the time spent reconciling it, before deciding that more parallel work helped.

For your next job, name the shared files first. They often tell you where the useful split is.

## do worktrees prevent all merge conflicts?

No. They separate working files, while branches can still change the same lines or disagree on an interface. Use the [review checklist](/blog/how-to-review-an-ai-generated-pull-request) on the combined change, even when Git merges it cleanly.


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