autodiscover.ignore_paths not respected during apply

[jholm117]

Description

autodiscover.ignore_paths correctly filters projects during atlantis plan, but atlantis apply (without -p) still discovers and attempts to apply projects in ignored paths.

Steps to Reproduce

1. Have a repo with modules sourced from a git repository (e.g., source = "git@github.com:org/modules.git//module-name?ref=abc123")
2. The module repo contains subdirectories with .tf files (e.g., test-deployment/main.tf) that are not actual deployable projects
3. When Terraform downloads the module, the entire repo lands under .terraform/modules/<name>/, including those extra directories
4. Configure atlantis.yaml with:

   autodiscover:
     mode: enabled
     ignore_paths:
       - ".terraform/**"

5. Run atlantis plan — correctly discovers only the intended projects
6. Run atlantis apply — discovers and attempts to apply the ignored paths, resulting in:

   no plan found at path "project/.terraform/modules/some_module/test-deployment" and workspace "default"–did you run plan?
   

Expected Behavior

atlantis apply should respect ignore_paths and only attempt to apply projects that were not filtered out.

Actual Behavior

atlantis apply picks up terraform roots inside ignored paths and fails with "no plan found" errors. The summary check (atlantis/apply) reports failures even though all real projects applied successfully.

Root Cause

The plan and apply code paths diverge in how they discover projects:

• Plan path (buildAllCommandsByCfg → getMergedProjectCfgs): calls isAutoDiscoverPathIgnored() to filter out ignored paths. Works correctly.
• Apply path (buildAllProjectCommandsByPlan): uses PendingPlanFinder.Find() which scans the working directory for terraform roots via git ls-files. This path never checks ignore_paths.

The fix would be to add ignore_paths filtering inside buildAllProjectCommandsByPlan() after PendingPlanFinder.Find() returns results, similar to what getMergedProjectCfgs() does for plan.

Environment

• Atlantis version: v0.33.0 (also confirmed by reading source through v0.40.0)
• ignore_paths feature introduced in v0.33.0 via feat: Add ignore path to autodiscover using glob #5267

[dosubot]

Hi @jholm117! I'm Dosu and I’m helping the atlantis team.

Your analysis is correct — I can confirm this is a bug. The root cause you identified is accurate:

• Plan path: buildAllCommandsByCfg() → getMergedProjectCfgs() calls isAutoDiscoverPathIgnored() at line 440 to filter out ignored paths.
• Apply path: buildAllProjectCommandsByPlan() uses PendingPlanFinder.Find() which only filters out .terragrunt-cache/ directories and has no ignore_paths integration.

This appears to be a previously unreported issue. PR #5849 recently fixed server-side ignore_paths config, but that only affects the plan path — not the apply path.

Your suggested fix (adding ignore_paths filtering in buildAllProjectCommandsByPlan() after PendingPlanFinder.Find() returns) aligns with the existing architecture and would be the cleanest approach.

To reply, just mention @dosu.

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Docs are dead. Just use Dosu.

[jholm117]

Hey @jamengual @lukemassa — any chance this could get a review? The fix is up at #6332, tests passing. We're running it in production on our fork and it's been working well. Happy to address any feedback.