Treatment of dangling symlinks in OpamFilename.files

[dra27]

Came up in #4641. OpamSystem.files_with_links doesn't return dangling symlinks (symlinks whose target does not exist) because Sys.file_exists returns false for these entries. There are some situations where this is wanted, and some where it definitely is not. I went through the locations - we should confirm the list and fix the ones which require it. There is OpamSystem.files_all_not_dir for this purpose.

• OpamAdminCommand.index_command - doesn't want dangling symlinks
• OpamAction.remove_package_aux - should consider them, it's a bug
• OpamAdminRepoUpgrade.do_upgrade - doesn't want dangling symlinks
• OpamListCommand.apply_selector - not sure
• OpamSwitchCommand.reinstall - wants dangling links
• OpamPinCommand.edit - wants dangling links
• OpamPackage.list and OpamPackage.prefixes - not sure
• OpamVCS.Make.sync_dirty - wants dangling symlinks ??
• OpamPinned.files_in_source - wants dangling symlinks ??
• OpamSwitchState.load - doesn't want dangling symlinks
• OpamFileTools.extra_files_default and OpamFileTools.add_aux_files - wants to have them and warn about them? or just ignore?!
• OpamFormatUpgrade.from_1_1_to_1_2 - probably wants to delete dangling symlinks ?!
• OpamFormatUpgrade.from_2_0_alpha3_to_2_0_beta - doesn't want dangling symlinks
• Opam_installer.options - doesn't want dangling symlinks