Yes, tools like diff and md5 would work and I expect will form the
components of any solution. I figured that one of the popular IDS
mechanisms might be well tuned for this use case, and that there'd be
some folks on list using some similar solution (hand-rolled or of an
existing project).

Things like tripwire, rkhunter, etc focus on system binaries by
default (some - I forget which - even go so far as to add a signature
to the ELF header). If they're focused on binaries, they may not be so
capable when handling executables for the web (by which I mean *.php
and friends).

Differences that spring to mind for web-based executables are: the
large number of cross-referenced include files; ability to exclude
cache directories (eg apps which generate cache-xxx.php files in a
specific directory); different maintenance requirements of accepting
(or not!) the fact that a customer has just uploaded 112 .inc and .php
files when they downloaded phpbb2.

So - my target here is easier management of a server where another
admin is installing sites and modules of a popular CMS (and I'd like
to be notified of what's being added), and notification if an intruder
modifies any existing file as well.
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