Environment:
NB 6.1-full Installed with default options to users folder with full permissions.
All available NB patches applied
Ubuntu Linux 8.04

Issue:
Due to the restriction on installing gems with native code imposed by the version of jruby included with the NB
installer, gems which require native extensions (generated using mkmf.rb) are not supported; however, some of these gems
(e.g.: ruby-debug-base, ruby-debug-ide) are part of the installation and as such, patched versions appear in the list of
gem updates.  When one of these gems is selected for update, or a gem that uses a native library is selected for update,
the update fails.

Here is an example from an attempt to update the ruby-debug-ide gem which requires an update of the ruby-debug-base gem:

Attempting remote update of ruby-debug-base
Installing gem ruby-debug-base-0.10.1
/home/user1/Apps/netbeans-6.1/ruby2/jruby-1.1/lib/ruby/gems/1.8/gems/ruby-debug-base-0.10.1/AUTHORS
/home/user1/Apps/netbeans-6.1/ruby2/jruby-1.1/lib/ruby/gems/1.8/gems/ruby-debug-base-0.10.1/CHANGES
/home/user1/Apps/netbeans-6.1/ruby2/jruby-1.1/lib/ruby/gems/1.8/gems/ruby-debug-base-0.10.1/LICENSE
/home/user1/Apps/netbeans-6.1/ruby2/jruby-1.1/lib/ruby/gems/1.8/gems/ruby-debug-base-0.10.1/README
/home/user1/Apps/netbeans-6.1/ruby2/jruby-1.1/lib/ruby/gems/1.8/gems/ruby-debug-base-0.10.1/Rakefile
/home/user1/Apps/netbeans-6.1/ruby2/jruby-1.1/lib/ruby/gems/1.8/gems/ruby-debug-base-0.10.1/ext/breakpoint.c
/home/user1/Apps/netbeans-6.1/ruby2/jruby-1.1/lib/ruby/gems/1.8/gems/ruby-debug-base-0.10.1/ext/extconf.rb
/home/user1/Apps/netbeans-6.1/ruby2/jruby-1.1/lib/ruby/gems/1.8/gems/ruby-debug-base-0.10.1/ext/ruby_debug.c
/home/user1/Apps/netbeans-6.1/ruby2/jruby-1.1/lib/ruby/gems/1.8/gems/ruby-debug-base-0.10.1/ext/ruby_debug.h
/home/user1/Apps/netbeans-6.1/ruby2/jruby-1.1/lib/ruby/gems/1.8/gems/ruby-debug-base-0.10.1/lib/ruby-debug-base.rb
/home/user1/Apps/netbeans-6.1/ruby2/jruby-1.1/lib/ruby/gems/1.8/gems/ruby-debug-base-0.10.1/lib/ChangeLog
/home/user1/Apps/netbeans-6.1/ruby2/jruby-1.1/lib/ruby/gems/1.8/gems/ruby-debug-base-0.10.1/test/base/base.rb
/home/user1/Apps/netbeans-6.1/ruby2/jruby-1.1/lib/ruby/gems/1.8/gems/ruby-debug-base-0.10.1/test/base/binding.rb
/home/user1/Apps/netbeans-6.1/ruby2/jruby-1.1/lib/ruby/gems/1.8/gems/ruby-debug-base-0.10.1/test/base/catchpoint.rb
Building native extensions.  This could take a while...
extconf.rb:1:in `require': no such file to load -- mkmf (LoadError)
	from extconf.rb:1
ERROR:  Error installing ruby-debug-base:
	ERROR: Failed to build gem native extension.

/home/user1/Apps/netbeans-6.1/ruby2/jruby-1.1/bin/jruby extconf.rb update --verbose --no-rdoc --no-ri

Gem files will remain installed in
/home/user1/Apps/netbeans-6.1/ruby2/jruby-1.1/lib/ruby/gems/1.8/gems/ruby-debug-base-0.10.1 for inspection.
Results logged to
/home/user1/Apps/netbeans-6.1/ruby2/jruby-1.1/lib/ruby/gems/1.8/gems/ruby-debug-base-0.10.1/ext/gem_make.out
Gems updated: ruby-debug-base


So as can be seen by the error message, the issue is the missing mkmf.rb file.  While we know that the mkmf issue has
been reported to jruby (http://jira.codehaus.org/browse/JRUBY-1036) and is marked as a "Won't Fix" item due to the
desire to avoid native code, this gem (and others) are necessarily exceptions since they are required by NetBeans and
other development environments to attach to the ruby process for debugging, and in some circumstances mandatory since
the NetBeans environment reports frequently that to debug jruby or ruby code, the Fast Debugger (ruby-debug-ide) is
required.


A