With the advent of the MANIFEST file, files which are rewritten when
deployed, such as those which have the GIT hash in the query string to force
browser reloading, were no longer deployed unless the content of those files
changed.

This patch adds a flag to the MANIFEST file to indicate that the file was
rewritten when it was deployed. This allows the file to be deployed and
rewritten again when the deployment is run, but also adds an indication
to the console output to distinguish deploying changes as opposed to
deploying rewrites.

(rather than deleted after install)

This allows the MANIFEST to be hidden from HTTP requests since the entire
include/ folder is already denied for Apache.

As an option, this will allow preventing deployment of files not tracked
with git. It's also about twice as fast as the PHP version.

This allows files which are edited on the fly during deployment to be
tracked so that they are not unnecessarily deployed again in the next
deployment run. It also allows for more creative deployment strategies using
something like `git ls-files -s`

Also, write js and css links to be forcibly reloaded by the browser after
deployment

Also, if any non-shipped .htaccess files exist, don't clean those either

Fixes #60

Allows the deploy script to remove files in the target that are not preset
in the current repository. This patch assumes pure stock osTicket
deployments -or- that the files deployed in the target are also present in
the local repository.

When the include path is written in bootstrap.php, ensure that extra slashes
are not accidentally added

Fixes #20

Useful for initial installs, where deployment of the `setup/` folder is
required for the initial install. Thereafter, deployment can be run without
the setup option so that the rest of the codebase can be maintained (already
supported)

This will allow an administrator to visualize the files changed in the
deployment before actually copying out the new files

This will allow folks following the git development model to checkout the
sourcecode to one folder, follow an upstream git brach, and deploy the
osticket installation from a current branch to a location somewhere.

The deploy process differs from the unpack process in that it does not
assume to be inside an 'upload/' folder from the install zipball, and it
does not deploy the 'setup/' folder.

The include folder is still supported to be installed elsewhere.