pkg does bad things after upgrade from 8.4 to 9.3

[Michael R. Wayne]

I brought this up on irc, did not get a helpful answer.

After upgrading a machine from 8.4 to 9.3, I went to upgrade 
ports/packages. Some need to be built from source as they 
use non-standard options but most should be installable directly
with pkg install.

Note that both pkg and pkg-devel exhibit the same problem.

Some install just fine. Others do NASTY things. 

Here, I show that zip installs properly. But bash wants to 
delete TOTALLY UNRELATED things (why would bash want to delete
mutt and apache?)
   http://www.wayne47.com/fbsd_issue.html

I then did a
   pkg update -F
which fetched the world, then wanted to reinstall everything (to
which I said no) and the problem continues:
   http://www.wayne47.com/fbsd3.html

It looks like, in part, pkg can not determine what files are installed:
   http://www.wayne47.com/fbsdbug.html

Is there some way I can force pkg to install individual packages and not
touch the unrelated things? This behaviour seems very flawed to me but
the irc chat suggests I'm missing something.

Guidance on how to proceed would be appreciated. Note, again, that
I can not simply pkg update all ports as some must be built from
source.