It's not a question of theology or flavors (or flavours). The issue
again comes back to basic, easily stated, easily learned, universally
followed principles. In Axiom
all files are literate.
all directories have Makefiles that handle their subtrees.
all Makefiles have a stanza per file (or used to)
all stanzas have unique identifing numbers
all non-axiom tools live under zips
all human written files live under SRC
all machine-generated, system-independent files live under INT
all machine-generated, system-dependent files live under OBJ
all final shipped files live under MNT.
all literate files use the same bibtex file or will once we get it working.
etc...