Using the terminal, I suppose you could do:
php apigen.phar generate --source xxx --destination xxx --exclude folder_to_excluse --exlude yet_another_folder
(its the same behavior with multiple sources)
I'm trying to exclude multiple folders in a .conf file, when I have the answer I'll update this answer :D, hope it helps.
-- Update --
To add multiple sources and/or multiple exclude references from a config file:
# Source file or directory to parse
source:
# ../PASTA
- ../sys
- ../anotherfolder
# Directory where to save the generated documentation
destination: 'C:\xampp\htdocs\yourfolder'
# List of allowed file extensions
extensions: [php]
# Mask to exclude file or directory from processing
exclude:
- '../sys/vendor'
- '..sys/core'
#next elements of the config file.
And to run the config file:
apigen generate --config file.conf