If you want to modify standard Eclipse plug-ins, you can use Feature Patch Projects. A Feature Patch Project can contain plug-ins which replace existing plug-ins. This would allow you to create an update site for this feature and users can use your version of the modified code.

Each feature can only be patched once.

A feature patch project can get created via File  New  Other…​  Plug-in Development  Feature Patch.

In this dialog select the feature which you want to patch. Add every modified plug-in to your new project and export it as a p2 update site to make it available.