If annotations.jar is missing, it maybe ADT 23 related problems.
Check this.
Update eclipse with Android Development tools 23
Google response:
...
and copy over the following files:
tools/hprof-conv
tools/support/annotations.jar
tools/proguard
(Added)
If its ADT bundle problem (part of ADT 23 related problem),
this part is for you. (Linked above)
Google response:
...
This is a packaging bug. The entire proguard file is missing. We'll have an update asap, but until then just copy it over from a previous version of the tools:
...
Edit: with the latest ADT release, the bundle should now work with auto-update, so install these new versions:
linux 64 bit vm: http://dl.google.com/android/adt/adt-bundle-linux-x86_64-20140702.zip
linux 32 bit vm: http://dl.google.com/android/adt/adt-bundle-linux-x86-20140702.zip
mac: http://dl.google.com/android/adt/adt-bundle-mac-x86_64-20140702.zip
win32: http://dl.google.com/android/adt/adt-bundle-windows-x86-20140702.zip
win64: http://dl.google.com/android/adt/adt-bundle-windows-x86_64-20140702.zip
Don't try to upgrade from previous version because it doensn't work at all. If you have got problems with zipalign, it's now under platform-tools and no more under tools/ so you can do a symbolic link or just copy it into the expected folder.
or use "not-bundled" Eclipse.
ADT23 problem related links
Issue 72400 (merged into 72419) getDefaultProguardFile no longer returns valid path using build SDK tools 23
Issue 72419 Proguard not installed with SDK tools rev. 23