When a JVP file is opened from command line without a --colour scheme specified, the preferences default colour scheme is applied overwriting the colour scheme saved in the JVP file

When a Jalview project file (JVP) is opened from the command line without a --colour scheme specified on the command line

e.g.
jalview examples/exampleFile_2_7.jar

the colour scheme saved in the JVP file changes to the colour scheme saved as default in .jalview_properties. This is set to "None" after the first time a user "OK"s the Preferences (with or without any changes), so appears to remove the colouring from existing colour schemes in the JVP.

Fix: When it's a JVP file, don't apply the user preference colour scheme if no --colour has been set.