make inputdir (sys.inputdir)  and masterdir (sys.masterdir)  configurable via configure options. Solve issue #3688
rewrite some if/else logic, thanks to @ediosyncratic
added some comment why not to use GetInputDir()
Fix PIDDIR containing a preceding '='.
Bring back Windows specific copy_from section in failsafe.cf.

It is needed because Windows looks in the wrong folder on the remote
host (Masterdir on Windows is C:\Program Files\Cfengine\masterfiles).
Merge branch 'configurable_workdirs' (Pull request #1293)

"make inputdir (sys.inputdir) and masterdir (sys.masterdir)
configurable"