scm and filesystem client are in th plain java libraries

none of this is in the sdk.. (well all the libs are duplicated there, but none is server side apis)

you can do everything to the scm system you want from the plainjava api.
some things you would have to re-invent however are

the pending changes monitor that is provided by eclipse. (background thread, polling the repo to check for changes)..
the scm commandline gives it to you one command at a time.

there are eclipse based extensions/wrappers (rcp...)  that make the services easier to consume for the eclipse plugin function, but underneath it calls the plain java api.

the *ide.ui' code is for managing the eclipse UI of the rtc plugin (create/edit a workitem, workspace, build, ...)

I don't know about many extension points on the client side..  but there seems to be support for adding/changing popup menus, drop downs, and some dialogs..

I have changed the product source (both sides, without doing a plugin extension) to do lots of different things..
enable a 'file system link' to attachments on a shared file system instead of the DB
enable a function to restrict new linktypes to specific projects, workitems.. (link to 'other workitem type', but only from defects or stories, not tasks, or stories, or epics)..