My only (systemwide) cb is the one from trunk. No cb launchpad package.
Before my plain old Makefile executes a make install, it
moves the existing directories /usr/local/lib/codeblocks and /usr/local/share/codeblocks away
to avoid having stale older files lying around there. Sor some other progs I use checkinstall,
but not (yet) for cb.
Did you execute ./bootstrap again as well?
my configure to build out of tree:
mkdir -p $(BUILDDIR)
(cd $(BUILDDIR) && ../$(SRCDIR)/configure --prefix=$(PREFIX) --with-contrib-plugins=all,-NassiShneiderman)
Can you use a spare computer or virtual machine with a fresh ubuntu?
Useful to automate the steps in the cb wiki for your machine.
You can write down the steps to do so into a simple Makefile.
From cloning, updating, installing prerequisites, bootstrap, config, make, make install.
Once you have that Makefile, starting that from scratch will become a lot easier.