The purpose of having all the different files described in the section
above is to avoid having the same information in more than one place. If
you change the installation directories or top-level prefix at
configure-time, those changes will propagate through the whole
sequence. And if you change the default paths in `texmf.cnf.in',
those changes are propagated to the compile-time defaults.
The Make definitions are all repeated in several Makefile's; but changing the top-level `Makefile' should suffice, as it passes down all the variable definitions, thus overriding the submakes. (The definitions are repeated so you can run Make in the subdirectories, if you should have occasion to.)
By default, the bitmap font paths end with `/$MAKETEX_MODE', thus including the device name (usually a Metafont mode name such as `ljfour'). This distinguishes two different devices with the same resolution--a write/white from a write/black 300dpi printer, for example.
However, since most sites don't have this complication, Kpathsea
(specifically, the kpse_init_prog function in
`kpathsea/proginit.c') has a special case: if the mode has not been
explicitly set by the user (or in a configuration file), it sets
MAKETEX_MODE to /. This makes the default PK path, for
example, expand into .../pk//, so fonts will be found even if
there is no subdirectory for the mode (if you arranged things that way
because your site has only one printer, for example) or if the program
is mode-independent (e.g., pktype).
To make the paths independent of the mode, simply edit `texmf.cnf.in' before installation, or the installed `texmf.cnf', and remove the `$MAKETEX_MODE'.
See section `MakeTeX' script arguments, for how this interacts with MakeTeXPK.
See section TeX directory structure, for a description of the default arrangement of the input files that comprise the TeX system. The file `kpathsea/HIER' is a copy of that section.
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