But there is stuff in the .bash_profile shipped by older versions of
Ubuntu that never gets run. So certain functionality stopped working on
upgrade, which seems like a regression to me.

For example, my desktop which now runs feisty, but was upgraded from
older versions of Ubuntu has the following at the top of the
~/.bash_profile:

# ~/.bash_profile: executed by bash(1) for login shells.
# see /usr/share/doc/bash/examples/startup-files for examples.
# the files are located in the bash-doc package.

This file used to be run on login, then at some point stopped being run
(Edgy I believe, but I could be wrong)

My laptop has a clean install of Feisty and the ~/.profile includes
~/.bash_profile if it exists, however the upgraded box never got a
~/.profile to do that include, meaning that the old .bash_profile no
longer runs.

The point being that whether it's a portable assumption or not, it's an
assumption that Ubuntu used to make and then dropped, causing people's
~/bin to stop being included in the path, which seems to me to be a
regression.

-- 
.bash_profile is not sources when X session starts
https://bugs.launchpad.net/bugs/66004
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