docs: refresh CI page with native CI workflows; deprecate legacy GH Actions

internal/exec/describe_affected.go

@@ -14,6 +14,7 @@ import (
 	"github.com/cloudposse/atmos/pkg/auth"
 	"github.com/cloudposse/atmos/pkg/ci"
 	cfg "github.com/cloudposse/atmos/pkg/config"
+	ghactions "github.com/cloudposse/atmos/pkg/github/actions"
 	log "github.com/cloudposse/atmos/pkg/logger"
 	"github.com/cloudposse/atmos/pkg/matrix"
 	"github.com/cloudposse/atmos/pkg/pager"
@@ -361,7 +362,13 @@ func (d *describeAffectedExec) view(a *DescribeAffectedCmdArgs, repoUrl string,
 	// Handle matrix format specially - it bypasses the normal view flow.
 	if a.Format == "matrix" {
 		entries := convertAffectedToMatrix(affected)
-		return matrix.WriteOutput(entries, a.GithubOutputFile)
+
+		// Resolve output file: explicit flag > CI auto-detect > stdout.
+		outputFile := a.GithubOutputFile
+		if outputFile == "" && d.atmosConfig.CI.Enabled {
+			outputFile = ghactions.GetOutputPath()
+		}
+		return matrix.WriteOutput(entries, outputFile)
 	}
 
 	// Reject --output-file for non-matrix formats — it would be silently ignored.

internal/exec/describe_affected_test.go

@@ -1880,6 +1880,73 @@ func TestExecute_MatrixFormat(t *testing.T) {
 		assert.Contains(t, string(content), "matrix=")
 		assert.Contains(t, string(content), "count=1")
 	})
+
+	t.Run("matrix auto-detects GITHUB_OUTPUT when CI is enabled", func(t *testing.T) {
+		// When ci.enabled=true and no explicit --output-file is given,
+		// the matrix output should be written to $GITHUB_OUTPUT automatically.
+		autoFile := filepath.Join(t.TempDir(), "auto_output")
+		t.Setenv("GITHUB_OUTPUT", autoFile)
+
+		dCI := d
+		dCI.atmosConfig = &schema.AtmosConfiguration{CI: schema.CIConfig{Enabled: true}}
+
+		err := dCI.Execute(&DescribeAffectedCmdArgs{
+			Format:    "matrix",
+			CLIConfig: &schema.AtmosConfiguration{CI: schema.CIConfig{Enabled: true}},
+		})
+		require.NoError(t, err)
+
+		content, err := os.ReadFile(autoFile)
+		require.NoError(t, err)
+		assert.Contains(t, string(content), "matrix=")
+		assert.Contains(t, string(content), "count=1")
+	})
+
+	t.Run("explicit --output-file wins over CI auto-detect", func(t *testing.T) {
+		// When both --output-file and CI auto-detect would apply, the explicit
+		// flag must win. The GITHUB_OUTPUT path should be left untouched.
+		explicitFile := filepath.Join(t.TempDir(), "explicit_output")
+		ghOutputFile := filepath.Join(t.TempDir(), "github_output")
+		t.Setenv("GITHUB_OUTPUT", ghOutputFile)
+
+		dCI := d
+		dCI.atmosConfig = &schema.AtmosConfiguration{CI: schema.CIConfig{Enabled: true}}
+
+		err := dCI.Execute(&DescribeAffectedCmdArgs{
+			Format:           "matrix",
+			GithubOutputFile: explicitFile,
+			CLIConfig:        &schema.AtmosConfiguration{CI: schema.CIConfig{Enabled: true}},
+		})
+		require.NoError(t, err)
+
+		content, err := os.ReadFile(explicitFile)
+		require.NoError(t, err)
+		assert.Contains(t, string(content), "matrix=")
+
+		// The GITHUB_OUTPUT path must NOT have been written to.
+		_, err = os.Stat(ghOutputFile)
+		assert.True(t, os.IsNotExist(err), "GITHUB_OUTPUT file should not exist when --output-file is set explicitly")
+	})
+
+	t.Run("no auto-detect when CI is disabled", func(t *testing.T) {
+		// When ci.enabled=false, GITHUB_OUTPUT should be ignored even if it's
+		// set in the environment. Output goes to stdout (unverifiable here, but
+		// we assert the GITHUB_OUTPUT file remains untouched).
+		ghOutputFile := filepath.Join(t.TempDir(), "github_output")
+		t.Setenv("GITHUB_OUTPUT", ghOutputFile)
+
+		dNoCI := d
+		dNoCI.atmosConfig = &schema.AtmosConfiguration{CI: schema.CIConfig{Enabled: false}}
+
+		err := dNoCI.Execute(&DescribeAffectedCmdArgs{
+			Format:    "matrix",
+			CLIConfig: &schema.AtmosConfiguration{CI: schema.CIConfig{Enabled: false}},
+		})
+		require.NoError(t, err)
+
+		_, err = os.Stat(ghOutputFile)
+		assert.True(t, os.IsNotExist(err), "GITHUB_OUTPUT file should not exist when CI is disabled")
+	})
 }
 
 // TestView_OutputFileRejectsNonMatrix tests that --output-file is rejected for non-matrix formats.

website/blog/2025-12-15-list-affected-command.mdx

@@ -113,7 +113,7 @@ atmos list affected --repo-path /tmp/target-repo --format json
 
 - [atmos list affected documentation](/cli/commands/list/affected)
 - [atmos describe affected documentation](/cli/commands/describe/affected)
-- [GitHub Actions integration](/integrations/github-actions/affected-stacks)
+- [Native CI for GitHub Actions](/ci)
 
 ## Get Involved
 

website/blog/2026-02-08-describe-affected-deleted-detection.mdx

@@ -156,5 +156,5 @@ jobs:
 
 - [Describe Affected Command](/cli/commands/describe/affected) - Full command reference
 - [List Affected Command](/cli/commands/list/affected) - Human-readable table view
-- [Affected Stacks GitHub Action](/integrations/github-actions/affected-stacks) - CI/CD integration
+- [Native CI in GitHub Actions](/ci) - CI/CD integration
 - [Component Inheritance](/design-patterns/inheritance-patterns/abstract-component) - Abstract component patterns

website/blog/2026-04-28-describe-affected-matrix-auto-output.mdx

@@ -0,0 +1,87 @@
+---
+slug: describe-affected-matrix-auto-output
+title: "describe affected --format=matrix auto-routes to GITHUB_OUTPUT"
+authors: [osterman]
+tags: [enhancement]
+---
+
+`atmos describe affected --format=matrix` now writes to `$GITHUB_OUTPUT` automatically when CI is enabled, matching the behavior already shipped for `atmos list instances --format=matrix`. No more `--output-file=$GITHUB_OUTPUT` boilerplate in workflow YAML.
+
+<!--truncate-->
+
+## What Changed
+
+When `ci.enabled: true` is set in `atmos.yaml` and `$GITHUB_OUTPUT` is present in the environment (i.e. you're running on GitHub Actions), the matrix JSON is written there automatically. The explicit `--output-file=$GITHUB_OUTPUT` flag is no longer required.
+
+Before:
+
+```yaml
+- id: affected
+  run: atmos describe affected --format=matrix --output-file=$GITHUB_OUTPUT
+```
+
+After:
+
+```yaml
+- id: affected
+  run: atmos describe affected --format=matrix
+```
+
+The same goes for `atmos list instances --format=matrix`, which already had this behavior. Both commands now resolve their output destination the same way: explicit `--output-file` flag wins; otherwise, fall back to `$GITHUB_OUTPUT` when CI is enabled; otherwise, write JSON to stdout.
+
+## Why This Matters
+
+Before this change, the two `--format=matrix` commands behaved differently — `list instances` auto-detected, `describe affected` didn't. Workflow authors had to remember which one needed the explicit flag. With this change the two commands are symmetric, the docs are simpler, and copy-pasted workflows from one command to the other don't silently break.
+
+It's also one fewer thing to type. The matrix output is the canonical pattern for fan-out workflows in GitHub Actions, and the explicit redirect was always boilerplate.
+
+## How to Use It
+
+Set `ci.enabled: true` in your `atmos.yaml`:
+
+```yaml
+ci:
+  enabled: true
+```
+
+Then use the matrix command without the `--output-file` flag in your workflow:
+
+```yaml
+jobs:
+  affected:
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/cloudposse/atmos:${{ vars.ATMOS_VERSION }}
+    outputs:
+      matrix: ${{ steps.affected.outputs.matrix }}
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - id: affected
+        run: atmos describe affected --format=matrix
+
+  deploy:
+    needs: affected
+    if: ${{ needs.affected.outputs.matrix != '' }}
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/cloudposse/atmos:${{ vars.ATMOS_VERSION }}
+    strategy:
+      matrix: ${{ fromJson(needs.affected.outputs.matrix) }}
+      fail-fast: false
+    steps:
+      - uses: actions/checkout@v6
+
+      - env:
+          COMPONENT: ${{ matrix.component }}
+          STACK: ${{ matrix.stack }}
+        run: atmos terraform deploy "$COMPONENT" -s "$STACK"
+```
+
+The explicit `--output-file` flag still works if you need it (writing to an arbitrary path, non-GitHub CI providers, etc.) — explicit always wins over auto-detection.
+
+## Get Involved
+
+See the full CI workflow patterns at [Native CI](/ci), including the new "Deploy Affected" and "Deploy All" examples. The two reference repos — [`cloudposse-examples/atmos-native-ci`](https://github.com/cloudposse-examples/atmos-native-ci) and [`atmos-native-ci-advanced`](https://github.com/cloudposse-examples/atmos-native-ci-advanced) — show end-to-end working pipelines you can clone and adapt.