How to deploy 'non-versioned files' during upgrades

[pbchase]

The redcap_deployment does not have a good method for deploying REDCap's "non-versioned files" during an upgrade. One will get messages like this:

While there are reasons this warning could be a false-positive, there are plenty more reasons why it is a legitimate alert that should be addressed. On this particular host, these files were out of date:

./Instructions.txt
./redcap/ehr.php
./redcap/index.php
./redcap/redcap_connect.php
./redcap/cron.php
./redcap/surveys/index.php
./redcap/api/index.php
./redcap/api/help/index.php

Instructions.txt is not a problem, but every other file is.

One possible solution is to use the redcapX.Y.Z.zip files instead of the redcapX.Y.Z_upgrade.zip. With the recent change that excludes the database.php file found inside redcapX.Y.Z_upgrade.zip during upgrade (commit # 9db03a2) this might be a viable solution.

[pbchase]

In a private conversation, Rob Taylor said:

...Database.php and hook_functions.php are the only files in the root directory that should not be overwritten that I am aware of. You personally may not have modified hook_functions.php from its original state, but others might...

I think we should default to not replacing hook_functions.php. If we do replace it, that should be an option controlled by a parameter in the INI file. This would conform with redcap_deployment's direction of waning support for hook frameworks as we grow module support.