vlc.desktop: the version in it refers to the standard version not VLC version.

       - don't process it with config.status
       - get rif of the duplicate application/x-matroska
   Pointed by kwizart

share/Makefile.am

 EXTRA_DIST = $(DIST_rsrc) \
-	applications/vlc.desktop.in \
 	$(skins2_default_vlt_FILES)
-MOSTLYCLEANFILES = $(nobase_pkgdata_DATA) $(nobase_data_DATA)
+MOSTLYCLEANFILES = $(nobase_pkgdata_DATA) 
 
 pkgdatadir = $(datadir)/vlc
 
@@ -22,11 +21,8 @@ nobase_dist_pkgdata_DATA = \
 	$(DIST_osdmenu_minimal)
 
 nobase_pkgdata_DATA = skins2/default.vlt
-nobase_data_DATA = applications/vlc.desktop
+nobase_dist_DATA = applications/vlc.desktop
 
-applications/vlc.desktop: applications/vlc.desktop.in $(top_builddir)/config.status
-	cd "$(top_builddir)" && \
-	$(SHELL) ./config.status --file=$(subdir)/applications/vlc.desktop
 
 DIST_rsrc = \
 	newres.h \

share/applications/vlc.desktop.in → share/applications/vlc.desktop

 [Desktop Entry]
 Encoding=UTF-8
-Version=@VERSION@
+Version=1.0
 Name=VLC media player
 Name[fr]=Lecteur multimédia VLC
 Comment=Universal movies and music player
@@ -14,4 +14,4 @@ Icon=vlc
 Terminal=false
 Type=Application
 Categories=Application;AudioVideo;Player;
-MimeType=video/dv;video/mpeg;video/x-mpeg;video/msvideo;video/quicktime;video/x-anim;video/x-avi;video/x-ms-asf;video/x-ms-wmv;video/x-msvideo;video/x-nsv;video/x-flc;video/x-fli;application/ogg;application/x-ogg;application/x-matroska;audio/x-mp3;audio/x-mpeg;audio/mpeg;audio/x-wav;audio/x-mpegurl;audio/x-scpls;audio/x-m4a;audio/x-ms-asf;audio/x-ms-asx;audio/x-ms-wax;application/vnd.rn-realmedia;audio/x-real-audio;audio/x-pn-realaudio;application/x-flac;audio/x-flac;application/x-shockwave-flash;misc/ultravox;application/x-matroska;audio/vnd.rn-realaudio;audio/x-pn-aiff;audio/x-pn-au;audio/x-pn-wav;audio/x-pn-windows-acm;image/vnd.rn-realpix;video/vnd.rn-realvideo;audio/x-pn-realaudio-plugin;
+MimeType=video/dv;video/mpeg;video/x-mpeg;video/msvideo;video/quicktime;video/x-anim;video/x-avi;video/x-ms-asf;video/x-ms-wmv;video/x-msvideo;video/x-nsv;video/x-flc;video/x-fli;application/ogg;application/x-ogg;application/x-matroska;audio/x-mp3;audio/x-mpeg;audio/mpeg;audio/x-wav;audio/x-mpegurl;audio/x-scpls;audio/x-m4a;audio/x-ms-asf;audio/x-ms-asx;audio/x-ms-wax;application/vnd.rn-realmedia;audio/x-real-audio;audio/x-pn-realaudio;application/x-flac;audio/x-flac;application/x-shockwave-flash;misc/ultravox;audio/vnd.rn-realaudio;audio/x-pn-aiff;audio/x-pn-au;audio/x-pn-wav;audio/x-pn-windows-acm;image/vnd.rn-realpix;video/vnd.rn-realvideo;audio/x-pn-realaudio-plugin;