Patch not work on compose service

[LovesAsuna]

To Reproduce

1. create a compose service
2. create a docker-compose.yaml on root
3. use this file as compose path
4. deploy

Current vs. Expected behavior

The file cannot be found during deployment, but it should exist after applying the patch

Provide environment information

Dokploy version: Version v0.28.8

Which area(s) are affected? (Select all that apply)

Docker Compose

Are you deploying the applications where Dokploy is installed or on a remote server?

Same server where Dokploy is installed

Additional context

Will you send a PR to fix it?

No

[dosubot]

Hi @LovesAsuna! I'm Dosu and I’m helping the dokploy team.

This looks like a confirmed sequencing bug in the deployment flow. Here's what's happening:

During deployCompose, the patch commands and the build commands are generated together but executed as a single shell script. The problem is that getBuildComposeCommand calls writeDomainsToCompose, which reads the compose file from disk in Node.js before the shell script runs [1]. This means:

1. Patches are generated as shell commands [2]
2. writeDomainsToCompose reads the original (un-patched) compose file in Node.js and serializes it to base64 [3]
3. The combined shell script executes — patches apply to disk, but then the domain injection step overwrites the compose file with the pre-patch content

So any file created or modified by a patch (including the compose file itself) gets effectively nullified by this overwrite.

This was made worse by PR #3835 [4], which removed the early-return guard for empty domains — meaning the compose file is now always read and rewritten even when no domains are configured.

Additionally, rebuildCompose doesn't call generateApplyPatchesCommand at all [5], so redeploys also skip patches entirely.

A potential fix would be to split Phase 2 into two separate execAsync calls — first apply patches, then (after patches are on disk) read the compose file and build:

// Phase 2a: Apply patches first
let patchCommand = "set -e;" + await generateApplyPatchesCommand(...);
await execAsync(patchCommand);

// Phase 2b: Now read the patched compose file and build
let buildCommand = "set -e;" + await getBuildComposeCommand(entity);
await execAsync(buildCommand);

The same patch application step should also be added to rebuildCompose.

To reply, just mention @dosu.

---

^{How did I do? Good | Irrelevant | Incorrect | Verbose | Hallucination | Report 🐛 | Other}