Q:

Eclipse plugin development: Is plugin update or uninstall/install really clean? 

While developing Nodeclipse, I found that some bugs don't arise immediately but after some time, when combination of updates, restarts happens. 
Is plugin update or uninstall/install really clean? 
I develop and use installing for update, then use newer version until I got time/idea to improve.  However as said above I ran into situation when Eclipse behaves differently after the new feature have been used for several days. 
Is there some information that must be read about plugin install life-cycle, that mentions some not so evident behavior. 
UPDATE: Some problem were in Autumn 2013 when we were switching to tycho build.  Also around that time Eclipse Kepler 4.3.1 was released. 

A:

No, they are not "clean".  Moreover when you do uninstall, no files are deleted, Eclipse would just prevent plugin from loading on the startup.  
If you really want to remove the plugin you need to 

Uninstall it via UI
Delete the plugin files in the file system
Remove plugin settings from workspace or create a new one. 

Here is some interesting info for you:

There is no mechanism within Eclipse to permanently and physically
  uninstall a feature and its plug-ins.  The process to physically and
  permanently remove an undesirable feature and its plug-ins is a manual
  process that should be done when Eclipse is not running.  In order to
  do, you will have to manually remove the files there associated with
  the feature from the eclipse/features directory and its plug-ins from
  the eclipse/plugins directory.  Be very cautious as to which files you
  delete, and always have a backup of your Eclipse directory.  If you
  remove the wrong files from these directories, you may have quite some
  trouble restoring your Eclipse to a stable state.  Therefore, unless
  your hard disk storage capacity is extraordinarily limited, it is
  recommended that you simply leave the physical files in place. 
Note that when manually removing plugins as described above, it is
  likely that some metadata will still cached by Eclipse.  This can lead
  to problems later on.  Running Eclipse with the -clean option may help
  with that, as it causes Eclipse to clean the cached metadata.  See the
  Running Eclipse help page for details about this option. 

Source: http://wiki.eclipse.org/FAQ_How_do_I_remove_a_plug-in%3F

