Search for Files [in more than One Directory]

RewriteEngine on

#   first try to find it in custom/...
#   ...and if found stop and be happy:
RewriteCond /your/docroot/dir1/%{REQUEST_FILENAME}  -f
RewriteRule  ^(.+)  /your/docroot/dir1/$1  [L]

#   second try to find it in pub/...
#   ...and if found stop and be happy:
RewriteCond /your/docroot/dir2/%{REQUEST_FILENAME}  -f
RewriteRule  ^(.+)  /your/docroot/dir2/$1  [L]

#   else go on for other Alias or ScriptAlias directives,
#   etc.
RewriteRule   ^(.+)  -  [PT]