Isn't all this caused by bogus entries in bundles.info? I noticed that some features reference wrong files. For example:
- in bundles.info I have:
org.eclipse.linuxtools.cdt.autotools,2.0.0.201102162051,dropins/cdt/eclipse/plugins/org.eclipse.linuxtools.cdt.autotools_2.0.0.201102162051.jar,4,false

while in dropins directory:

root (18:21:41):pwd
/usr/lib/eclipse/dropins/cdt/eclipse/plugins
root (18:21:45):ls -l | grep autotools
-rw-r--r-- 1 root root   167819 May 26 20:11 org.eclipse.linuxtools.cdt.autotools_2.0.0.201105261810.jar
-rw-r--r-- 1 root root   227369 May 26 20:11 org.eclipse.linuxtools.cdt.autotools.core_1.0.1.201105261810.jar
drwxr-xr-x 6 root root     4096 Jun 15 17:47 org.eclipse.linuxtools.cdt.autotools_docs_2.0.2.201105261810
-rw-r--r-- 1 root root   655188 May 26 20:11 org.eclipse.linuxtools.cdt.autotools.ui_1.0.1.201105261810.jar

PS. I tried to analyze this and came up with following results:

root (18:41:23):awk -F"," '{ if( system( "[ -e /usr/lib/eclipse/" $3 " ] " ) != 0) { print $3 } }' bundles.info 
dropins/cdt/eclipse/plugins/org.eclipse.linuxtools.cdt.autotools_2.0.0.201102162051.jar
dropins/cdt/eclipse/plugins/org.eclipse.linuxtools.cdt.autotools.core_1.0.1.201102162051.jar
dropins/cdt/eclipse/plugins/org.eclipse.linuxtools.cdt.autotools.ui_1.0.1.201102162051.jar
dropins/cdt/eclipse/plugins/org.eclipse.linuxtools.cdt.autotools_docs_2.0.2.201102162051/
dropins/cdt/eclipse/plugins/org.eclipse.linuxtools.cdt.libhover_1.0.3.201102162051.jar
dropins/cdt/eclipse/plugins/org.eclipse.linuxtools.cdt.libhover.glibc_1.0.1.201102162051/
dropins/cdt/eclipse/plugins/org.eclipse.linuxtools.cdt.libhover.library_docs_1.0.1.201102162051/
dropins/cdt/eclipse/plugins/org.eclipse.linuxtools.cdt.libhover.libstdcxx_1.0.0.201102162051.jar

This list shows (hopefully :-) ) what files are missing

Your bundles.info file does indeed appear to have errors.  It should have been updated on the next usage of the Fedora system eclipse platform after the CDT update.  It looks at timestamps in a set of the dropin subdirectories to determine if an update is required.

To have it regenerate bundles.info, you could touch the cdt subdirectory as root under the system dropins folder.  Note, that if you do a future -V (verify) of the rpm package, it will note the discrepancy of the timestamp.  After touching, invoking the system eclipse should update bundles.info properly.

If this does not occur, please reply and indicate the version of the installed eclipse platform you are using.  Also indicate whether bundles.info was regenerated by checking its timestamp.

I was able to update eclipse-cdt from 7.0.1-5 to 7.0.1-7 with no errors and the bundles.info file was correctly updated under my ~/.eclipse directory.  Like you, I am using a Fedora 14 i386 system.  

Note, that if you had a Fedora Eclipse installation and then installed the CDT and Autotools/Libhover via the update site, then installed the CDT from Fedora, this is not supported.  I don't think that is the case here, but I mention it nonetheless.

Nope, on my system bundles.info (to be precise: /usr/lib/eclipse/configuration/org.eclipse.equinox.simpleconfigurator/bundles.info) was not changed even after I'd modified timestamp of dropins/cdt directory.

pwd
/usr/lib/eclipse/dropins 

ls -al cdt
total 12
drwxr-xr-x. 3 root root 4096 Aug 17 16:46 .
drwxr-xr-x. 9 root root 4096 Aug 17 16:06 ..
drwxr-xr-x. 4 root root 4096 Jun 15 17:47 eclipse

pwd
/usr/lib/eclipse/configuration/org.eclipse.equinox.simpleconfigurator

ls -al org.eclipse.equinox.simpleconfigurator 
total 80
drwxr-xr-x. 2 root root  4096 Jul  1 19:30 .
drwxr-xr-x. 7 root root  4096 Jun 11 22:05 ..
-rw-r--r--. 1 root root 69798 Jul  1 19:30 bundles.info

Furthermore, I have no such file under ~/.eclipse/ 
ls -al /home/rzeznik/.eclipse/155965261/configuration/org.eclipse.equinox.simpleconfigurator/
total 8
drwxrwxr-x 2 rzeznik rzeznik 4096 Jul  1 18:00 .
drwxrwxr-x 9 rzeznik rzeznik 4096 Aug 17 16:47 ..

(In reply to comment #4)
> Nope, on my system bundles.info (to be precise:
> /usr/lib/eclipse/configuration/org.eclipse.equinox.simpleconfigurator/bundles.info)
> was not changed even after I'd modified timestamp of dropins/cdt directory.

The system-wide bundles.info will not get modified; only the one in your home directory gets touched.

> Furthermore, I have no such file under ~/.eclipse/ 

find ~/.eclipse -name bundles.info ?

This bug is against Fedora 14. I'm closing it now please reopen if it still can be reproduced with supported Fedora version.