fix(scripts): resolve exclude_inherited_files bugs in profile file ha…

[fgrehm]

Summary

Fixes two bugs where exclude_inherited_files in profile config was ignored, causing excluded standards to still be processed.

Details

Both bugs used pipes that created subshells where excluded="true" didn't persist:

• Bug 1: Subshell variable scope in get_profile_files() - exclusions ignored when generating Claude Code Skills
• Bug 2: Missing exclusion check in get_profile_file() - files from current profile returned without checking exclusions

Fix: Replace pipes with process substitution and add exclusion check before returning files from current profile.

Linked item

• Fixes Agent OS should not install skills for standards which are excluded #240

Checklist

• Linked to related Issue/Discussion
• Documented steps to test (below)
• Drafted "how to use" docs (if this adds new behavior) - N/A, bug fix only
• Backwards compatibility considered (notes if applicable) - Fully backwards compatible, fixes existing functionality

Documented steps to test

1. Create a profile that excludes standards:

   # profiles/test-profile/profile-config.yml
   inherits_from: default
   exclude_inherited_files:
     - standards/backend/*
     - standards/frontend/*

2. Install the profile with Skills mode enabled:

   ~/agent-os/scripts/project-install.sh --profile test-profile \
     --standards-as-claude-code-skills true --dry-run

3. Verify output does NOT include backend/frontend skills:

   # Should NOT see:
   # .claude/skills/backend-*/SKILL.md
   # .claude/skills/frontend-*/SKILL.md
   
   # Should only see skills for included standards

4. Without the fix, backend/frontend skills are incorrectly created. With the fix, they are properly excluded.

Notes for reviewers

File changed: scripts/common-functions.sh (27 insertions, 9 deletions)

Changes made:

1. get_profile_files() function - Fixed subshell bug:

-                echo "$excluded_patterns" | while read pattern; do
+                while read pattern; do
                     if [[ -n "$pattern" ]] && match_pattern "$relative_path" "$pattern"; then
                         excluded="true"
                         break
                     fi
-                done
+                done <<< "$excluded_patterns"

2. get_profile_file() function - Added exclusion check before returning files from current profile:

 # Check if file exists in current profile
 if [[ -f "$full_path" ]]; then
+    # Check if this file is excluded (even in current profile)
+    if [[ -f "$profile_config" ]]; then
+        local excluded="false"
+        while read pattern; do
+            if [[ -n "$pattern" ]] && match_pattern "$file_path" "$pattern"; then
+                excluded="true"
+                break
+            fi
+        done < <(get_yaml_array "$profile_config" "exclude_inherited_files")
+
+        if [[ "$excluded" == "true" ]]; then
+            echo ""
+            return
+        fi
+    fi
     echo "$full_path"
     return
 fi

3. get_profile_file() function - Also fixed subshell bug in inheritance exclusion check (same pattern as 1.)

Technical notes:

• Pipes create subshells, so variable assignments don't persist. Process substitution (< <(...) or <<< "$var") keeps the loop in the current shell.
• Previously, files in the current profile were returned without checking exclusions - now they're checked regardless of location.

Testing: Verified with a profile that excludes backend and frontend standards - confirmed excluded skills are not created and excluded files are not copied.

Impact: Low risk - fixes broken functionality, no behavior change for profiles without exclusions.

[smaugho]

I had no luck with this solution, but after a lot of debugging, realized the problem was with bash running on Windows, for this to work here, I had to remove carriage return in the get_yaml_array()

                if (indent == array_indent) {
                    sub(/^-[[:space:]]*/, "")
                    # Remove quotes if present
                    gsub(/^["'\'']/, "")
                    gsub(/["'\'']$/, "")
                    <<added this
                    # Remove carriage returns (Windows line endings)
                    gsub(/\r/, "")
                    >>
                    print
                }

[CasJam]

thanks!