[Droid Incredible Android Development] jermaine151:
I've got this ripped apart and I'm about to compare it to what we had as the "official".

EDIT: It looks like they made changes to all of the framework files and a few others. I'll have to decompile and take a closer look. Here's the changelist from my original 605.3 OTA zip:

Files WORKING_091511_111749//boot.img and ../temp//boot.img differ
Only in ../temp/: installbusybox
Only in ../temp//META-INF: CERT.RSA
Only in ../temp//META-INF: CERT.SF
Only in ../temp//META-INF/com/google/android: update-binary
Only in ../temp//META-INF/com/google/android: updater-script
Only in WORKING_091511_111749//META-INF/com/google/android: update-script
Only in ../temp//META-INF: MANIFEST.MF
Files WORKING_091511_111749//system/app/EPST.apk and ../temp//system/app/EPST.apk differ
Files WORKING_091511_111749//system/app/FieldTrial.apk and ../temp//system/app/FieldTrial.apk differ
Files WORKING_091511_111749//system/app/Settings.apk and ../temp//system/app/Settings.apk differ
Only in ../temp//system/app: Superuser.apk
Files WORKING_091511_111749//system/app/VCast.apk and ../temp//system/app/VCast.apk differ
Files WORKING_091511_111749//system/app/VzNav.apk and ../temp//system/app/VzNav.apk differ
Files WORKING_091511_111749//system/app/VZWInstaller.apk and ../temp//system/app/VZWInstaller.apk differ
Files WORKING_091511_111749//system/app/VzwLBSPerm.apk and ../temp//system/app/VzwLBSPerm.apk differ
Only in ../temp//system/bin: su
Files WORKING_091511_111749//system/framework/am.jar and ../temp//system/framework/am.jar differ
Files WORKING_091511_111749//system/framework/android.policy.jar and ../temp//system/framework/android.policy.jar differ
Files WORKING_091511_111749//system/framework/android.test.runner.jar and ../temp//system/framework/android.test.runner.jar differ
Files WORKING_091511_111749//system/framework/bmgr.jar and ../temp//system/framework/bmgr.jar differ
Files WORKING_091511_111749//system/framework/bouncycastle.jar and ../temp//system/framework/bouncycastle.jar differ
Files WORKING_091511_111749//system/framework/com.android.location.provider.jar and ../temp//system/framework/com.android.location.provider.jar differ
Files WORKING_091511_111749//system/framework/com.google.translate.jar and ../temp//system/framework/com.google.translate.jar differ
Files WORKING_091511_111749//system/framework/com.htc.android.easopen.jar and ../temp//system/framework/com.htc.android.easopen.jar differ
Files WORKING_091511_111749//system/framework/com.htc.android.pimlib.jar and ../temp//system/framework/com.htc.android.pimlib.jar differ
Files WORKING_091511_111749//system/framework/com.htc.commonctrl.jar and ../temp//system/framework/com.htc.commonctrl.jar differ
Files WORKING_091511_111749//system/framework/com.htc.framework.jar and ../temp//system/framework/com.htc.framework.jar differ
Files WORKING_091511_111749//system/framework/com.htc.rss.jar and ../temp//system/framework/com.htc.rss.jar differ
Files WORKING_091511_111749//system/framework/com.orange.authentication.simcard.jar and ../temp//system/framework/com.orange.authentication.simcard.jar differ
Files WORKING_091511_111749//system/framework/com.scalado.util.ScaladoUtil.jar and ../temp//system/framework/com.scalado.util.ScaladoUtil.jar differ
Files WORKING_091511_111749//system/framework/core.jar and ../temp//system/framework/core.jar differ
Files WORKING_091511_111749//system/framework/core-junit.jar and ../temp//system/framework/core-junit.jar differ
Files WORKING_091511_111749//system/framework/ext.jar and ../temp//system/framework/ext.jar differ
Files WORKING_091511_111749//system/framework/framework.jar and ../temp//system/framework/framework.jar differ
Files WORKING_091511_111749//system/framework/ime.jar and ../temp//system/framework/ime.jar differ
Files WORKING_091511_111749//system/framework/input.jar and ../temp//system/framework/input.jar differ
Files WORKING_091511_111749//system/framework/javax.obex.jar and ../temp//system/framework/javax.obex.jar differ
Files WORKING_091511_111749//system/framework/monkey.jar and ../temp//system/framework/monkey.jar differ
Files WORKING_091511_111749//system/framework/pm.jar and ../temp//system/framework/pm.jar differ
Files WORKING_091511_111749//system/framework/services.jar and ../temp//system/framework/services.jar differ
Files WORKING_091511_111749//system/framework/sqlite-jdbc.jar and ../temp//system/framework/sqlite-jdbc.jar differ
Files WORKING_091511_111749//system/framework/svc.jar and ../temp//system/framework/svc.jar differ
Only in ../temp//system/xbin: busybox

EDIT: I wouldn't be surprised if they FINALLY fixed the GPS nag message because they definitely made changes in that file:

Files Settings.1st/smali/com/android/settings/HtcCdmaFeatureReceiver.smali and Settings.2nd/smali/com/android/settings/HtcCdmaFeatureReceiver.smali differ