[github] - several fixes to PluginsManager.php

🚑 fix(PluginsManager): several fixes

fusiondirectory-plugins-manager does not honour config file location other than /etc/fusiondirectory/fusiondirectory.conf
fix "Undefined index: help" on commandline option array
fix installation of plugins which use files in export/ and generic/ directories

This MR has two part

1. The usage of potential multiple configuration file if two FD are installed on the same OS.
2. The resolution of problems for plugins having export and generic directories.

The second problem will be treated directly, contribution is accepted as-is.

The first point will be treated within it own issue later on, ticket open: here

Original github issue : here