I am working with NB 4.1 EA - build 041014

This bug may be a Java and/or MDR bug.

I was trying to work with the Apache Beehive
sources, you can download them from
http://incubator.apache.org/beehive/

That source tree is pretty massive with many many
src roots. It includes many, many source files
that contain many Java 1.5 constructs, many
annotations in particular. It also contains some
Web App sources as well. And many, many ant scripts.

Before I get to the bug, let me explain how I was
working fine before I encountered the bug.

Initially, I created a simple J2SE project with
existing ant script and targeted the ultimate root
node build.xml for the entire source tree. Because
of the way I defined the project, the project tab
only shows the build.xml file. The remaining
sources are only visible under the NB Filesystems
tab, not in the project tab. 

I am noting this because with that project
organization, there were no
CreationFailedExceptions. And I was able to browse
the sources via the Filesystem successfully.

So far so good. However, I wanted to debug some
code, so I tried to create some additional
projects (also Java Project with Existing Ant
Script) and pointed to deeper sections of the
Beehive source tree, to actually define a project
with properly designated "Source Package Folder".
I also defined a Web Application with Existing
Sources", also pointing to a sub section of the
large Beehive source tree.

These new projects did include the NB 4 style
substructure of "Source Packages". 

However, the Classpath Scan reported numerous
CreationFailedExceptions. See attached
messages.log files.

These exceptions became so annoying that I first I
tried to unmount the new projects, but I was
competing for attention with the processing that
kept generating the CreationFailedExceptions.
Finally I tried to shut down studio. The shut down
process just slowed to a crawl, it was 10 minutes
trying to persist the classpath info to disk.
While it was doing this my Windows system was
nearly unusable because the CPU priority taken by
the NB process was preventing anything else from
getting CPU time. My mouse latency was totally out
of control.  Finally, I killed the process, and
this itself took several minutes to complete. It
was bad.

After that, I deleted the contents of
.netbeans\4.1ea1\var\cache and restarted the
studio. It started ok, but recall that before the
last shutdow, I had unmounted the troublesome
projects.

As I write this I have remounted those troublesome
projects and I am not getting the same exceptions.
So I am not sure how reproducible this situations
is, but it was completely debilitating when it
occurred. 

Please see attached message.log's for details.