Agent OS should not install skills for standards which are excluded

[chadpav]

Just found Agent OS and using the latest version 2.1.0

Reproduction

My profile configuration (as recommended): default (untouched) -> general (doesn't do anything) -> flutter (excludes a bunch of standards that aren't relevant)

In my flutter profile I've excluded all backend and frontend standards (since they assumed HTML mostly).

inherits_from: general

# Uncomment and modify to exclude specific inherited files:
exclude_inherited_files:
  - standards/backend/api.md
  - standards/backend/migrations.md
  - standards/backend/models.md
  - standards/backend/queries.md
  - standards/frontend/accessibility.md
  - standards/frontend/css.md
  - standards/frontend/components.md
  - standards/frontend/responsive.md

I run the project install script inside my flutter project:
~/agent-os/scripts/project-install.sh --profile flutter

Results

1. Only inherited standards are installed in the agent-os project folder (correct)
2. All skills are installed in .claude/skills from the default profile (incorrect)
   NOTE: The skills from the excluded standards have a reference to a non-existent file.

Solution?

I asked Claude to review your scripts and it found a bug in the shared shell scripts. It's working on my machine now but hoping to share this back to the repo.

 I'll analyze the profile file resolution logic to understand why excluded skills are being installed.

⏺ I found two significant bugs in the profile file handling:

  Bug 1: Broken Exclusion Check in get_profile_files (lines 426-432)

  The exclusion check has a subshell variable scope bug:

  # Check if excluded
  excluded="false"
  echo "$excluded_patterns" | while read pattern; do
      if [[ -n "$pattern" ]] && match_pattern "$relative_path" "$pattern"; then
          excluded="true"  # ❌ This runs in a subshell due to the pipe
          break
      fi
  done

  if [[ "$excluded" != "true" ]]; then  # ❌ Always false - variable unchanged

  The while read loop runs in a subshell because of the pipe (echo ... |). When excluded="true" is set inside
  the subshell, that change doesn't persist to the parent shell. So excluded is always "false" after the loop,
  meaning excluded files are never filtered out.

⏺ Bug 2: Timing of Exclusion Check in get_profile_file (lines 311-342)

  The exclusion logic is checked after finding a file in the current profile:

  # Check if file exists in current profile
  if [[ -f "$full_path" ]]; then
      echo "$full_path"  # ❌ Returns immediately without checking exclusions
      return
  fi

  # ... later ...

  # Check if file is excluded (only reached if file NOT in current profile)
  local excluded=$(get_yaml_array "$profile_config" "exclude_inherited_files" | while read pattern; do
      if match_pattern "$file_path" "$pattern"; then
          echo "yes"
          break
      fi
  done)

  The exclusion check only prevents inheritance from parent profiles. If a file exists in the current profile
  directory, it's returned immediately without checking if it should be excluded.

  Why This Causes Your Issue

  1. get_profile_files calls with "standards" subdirectory at line 194
  2. Due to Bug 1, ALL standards files from your profile (including ones in exclusion patterns) are returned
  3. For each file, install_standards calls get_profile_file at line 183
  4. Due to Bug 2, if the file exists locally, it's returned regardless of exclusions
  5. The file gets copied and installed

⏺ The Fix

  The subshell bug in get_profile_files needs to be fixed. The exclusion check should use process substitution
  instead of a pipe to avoid creating a subshell:

  # Current (broken):
  excluded="false"
  echo "$excluded_patterns" | while read pattern; do
      if [[ -n "$pattern" ]] && match_pattern "$relative_path" "$pattern"; then
          excluded="true"
          break
      fi
  done

  # Fixed version:
  excluded="false"
  while read pattern; do
      if [[ -n "$pattern" ]] && match_pattern "$relative_path" "$pattern"; then
          excluded="true"
          break
      fi
  done <<< "$excluded_patterns"

  This is at common-functions.sh:426-432.

  Would you like me to implement this fix?

> yes 
  ⎿  ⧉ Selected 1 lines from scripts/project-install.sh in Visual Studio Code

⏺ I'll fix both bugs in the common-functions.sh file.

⏺ Update(scripts/common-functions.sh)
  ⎿  Updated scripts/common-functions.sh with 2 additions and 2 removals                                   
       424    
       425                    # Check if excluded
       426                    excluded="false"
       427 -                  echo "$excluded_patterns" | while read pattern; do
       427 +                  while read pattern; do
       428                        if [[ -n "$pattern" ]] && match_pattern "$relative_path" "$pattern"; then
       429                            excluded="true"
       430                            break
       431                        fi
       432 -                  done
       432 +                  done <<< "$excluded_patterns"
       433    
       434                    if [[ "$excluded" != "true" ]]; then
       435                        # Check if already in list (override scenario)

⏺ Now I'll fix the second bug in get_profile_file where exclusions are only checked during inheritance, not
  when the file exists in the current profile:

⏺ Update(scripts/common-functions.sh)
  ⎿  Updated scripts/common-functions.sh with 17 additions                                             
       309    
       310            # Check if file exists in current profile
       311            if [[ -f "$full_path" ]]; then
       312 +              # Check if this file is excluded in the current profile
       313 +              local profile_config="$profile_dir/profile-config.yml"
       314 +              if [[ -f "$profile_config" ]]; then
       315 +                  local excluded="false"
       316 +                  while read pattern; do
       317 +                      if [[ -n "$pattern" ]] && match_pattern "$file_path" "$pattern"; then
       318 +                          excluded="true"
       319 +                          break
       320 +                      fi
       321 +                  done < <(get_yaml_array "$profile_config" "exclude_inherited_files")
       322 +  
       323 +                  if [[ "$excluded" == "true" ]]; then
       324 +                      echo ""
       325 +                      return
       326 +                  fi
       327 +              fi
       328 +  
       329                echo "$full_path"
       330                return
       331            fi

⏺ I also need to fix the same subshell bug in the inheritance exclusion check later in the same function:

⏺ Update(scripts/common-functions.sh)
  ⎿  Updated scripts/common-functions.sh with 6 additions and 5 removals                                  
       346            fi
       347    
       348            # Check if file is excluded
       349 -          local excluded=$(get_yaml_array "$profile_config" "exclude_inherited_files" | while 
           - read pattern; do
       350 -              if match_pattern "$file_path" "$pattern"; then
       351 -                  echo "yes"
       349 +          local excluded="false"
       350 +          while read pattern; do
       351 +              if [[ -n "$pattern" ]] && match_pattern "$file_path" "$pattern"; then
       352 +                  excluded="true"
       353                    break
       354                fi
       355 -          done)
       355 +          done < <(get_yaml_array "$profile_config" "exclude_inherited_files")
       356    
       357 -          if [[ "$excluded" == "yes" ]]; then
       357 +          if [[ "$excluded" == "true" ]]; then
       358                echo ""
       359                return
       360            fi

⏺ Perfect! I've fixed both bugs in /Users/chadpavliska/agent-os/scripts/common-functions.sh.

  What Was Wrong

  Bug 1: Subshell Variable Scope Issue (3 locations)
  The code used pipes (echo "$patterns" | while read) which created subshells. When excluded="true" was set
  inside the subshell, the change never persisted to the parent shell, so excluded files were never actually
  filtered out.

  Bug 2: Exclusion Check Timing
  In get_profile_file, when a file existed in the current profile, it was returned immediately without checking
   if it should be excluded. The exclusion check only ran during inheritance lookups.

  The Fixes

  1. common-functions.sh:427-432 - Fixed get_profile_files subshell bug by using <<< "$excluded_patterns"
  instead of piping
  2. common-functions.sh:312-327 - Added exclusion check when file exists in current profile (before returning
  it)
  3. common-functions.sh:349-360 - Fixed inheritance exclusion check subshell bug by using process substitution
   < <(get_yaml_array ...)

  Now when you run install_standards(), it will:
  1. Get the list of standards files (properly excluding patterns from exclude_inherited_files)
  2. For each file, check if it should be excluded before installing it
  3. Only install standards files that are NOT in your profile's exclusion list

  The fix ensures that exclusion patterns in profile-config.yml are properly respected at both the file
  discovery and file resolution stages.

[fgrehm]

I opened a PR for this: #248. Also related: #247