Project file (jvp) saved formatting is not necessarily respected when opened on the command line

When a JVP is opened from the command line, the formatting saved at the time of the project file (e.g. Hide Annotations) reverts to the user's default preferences (unless specified on the command line).

This is probably because the command line assumes defaults if the argument is not specified and applies it to the AlignFrame opened.
Fix: When a JVP file is detected in the command line these formatting options should only be used if actually specified.