diff --git a/action.yml b/action.yml
index 8754a97..4473fb6 100644
--- a/action.yml
+++ b/action.yml
@@ -38,10 +38,10 @@ inputs:
     required: false
     default: 'true'
 
-  target:
-    description: "Configuration name"
+  command:
+    description: "Atmos command to generate readme"
     required: true
-    default: 'readme'
+    default: 'docs generate readme'
 
   validate_readme:
     required: false
@@ -232,15 +232,20 @@ runs:
       env:
         GITHUB_TOKEN: "${{ inputs.token }}"
       run: |
-        output_file=$(atmos docs generate ${{ inputs.target }} 2>&1 | sed -n -e  "s/^.*output=//p")
-        # Get relative path from absolute
-        output_file=$(realpath -s --relative-to="$PWD" "$output_file")
-        # Ignore changes if they are only whitespace
-        if ! git diff --quiet ${output_file} && git diff --ignore-all-space --ignore-blank-lines --quiet ${output_file}; then
-          git restore ${output_file}
-          echo Ignoring whitespace-only changes in generated file
-        fi
-        echo "file=${output_file}" >> $GITHUB_OUTPUT
+        set +e
+        atmos ${{ inputs.command }}
+        # Get all changed files and process them
+        changed_files=$(git status --porcelain | grep -E "^\s?(M|\?\?)" | cut -c4-)
+        set -e
+        for file in $changed_files; do
+          # Ignore changes if they are only whitespace
+          if ! git diff --quiet "$file" && git diff --ignore-all-space --ignore-blank-lines --quiet "$file"; then
+            git restore "$file"
+            echo "Ignoring whitespace-only changes in generated file: $file"
+          fi
+        done
+        files="$(echo ${changed_files})"
+        echo "file=${files// /,}" >> $GITHUB_OUTPUT
 
     - uses: gaurav-nelson/github-action-markdown-link-check@v1
       if: inputs.readme_enabled == 'true' && inputs.validate_readme == 'true'
@@ -300,10 +305,7 @@ runs:
         committer: ${{ inputs.commit_author }}
         sign-commits: ${{ inputs.sign-commits }}
         add-paths: |
-          ${{ steps.banner.outputs.file }}
-          ${{ steps.readme.outputs.file }}
-          **/README.md
-          docs/*
+          ${{ steps.banner.outputs.file }},${{ steps.readme.outputs.file }}
         body: |-
           ## what
           This is an auto-generated PR that updates the README.md and docs