You are right,  it does read the home directory first.

I figured out the problem was that for loading newer versions of files
over old ones, the files must be in the correct directory structure i.e.
"~/texmf/tex/latex".

I have just been putting files in "~/texmf/tex" and "~/texmf/bib" for
the past years.

perhaps i did not need to load newer versions of packages when using
tetex or tetex was more lax about this.

sorry for the irrelevant bug.

-- 
packages in ~/texmf should have priority over base system
https://bugs.launchpad.net/bugs/332167
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