New task md-files in miga doctor

lib/miga/cli/action/doctor.rb

@@ -49,6 +49,7 @@ def perform
     # TODO Implement this check:
     # refdb:  ['ref-db', 'Check index format of reference databases'],
     status: ['status', 'Update metadata status of all datasets'],
+    mdfiles:['md-files', 'Remove unregistered files in metadata'],
     db:     ['databases', 'Check integrity of database files'],
     dist:   ['distances', 'Check distance summary tables'],
     bidir:  ['bidirectional', 'Check distances are bidirectional'],

lib/miga/cli/action/doctor/operations.rb

@@ -65,6 +65,24 @@ def check_files(cli)
     cli.say
   end
 
+  ##
+  # Perform md-files operation with MiGA::Cli +cli+
+  def check_mdfiles(cli)
+    cli.say 'Looking for unregistered files in the metadata folder'
+    md = File.join(cli.load_project.path, 'metadata')
+    Dir.each_child(md) do |file|
+      expected_ds = File.basename(file, '.json')
+      next if cli.load_project.dataset_names.include?(expected_ds)
+      file_path = File.join(md, file)
+      if Dir.exist?(file_path)
+        cli.say "  > Ignoring directory: #{file}"
+      else
+        cli.say "  > Removing: #{file}"
+        File.unlink(File.join(md, file))
+      end
+    end
+  end
+
   ##
   # Perform cds operation with MiGA::Cli +cli+
   def check_cds(cli)

lib/miga/version.rb

@@ -12,7 +12,7 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.3, 15, 12].freeze
+  VERSION = [1.3, 16, 0].freeze
 
   ##
   # Nickname for the current major.minor version.