In my project I dynamically create the .qrc file based on which .qml files are part of the project like so

RESOURCE_CONTENT = \
    "<RCC>" \
    "<qresource prefix=\"/\">"
for(resourcefile, INCLUDED_RESOURCE_FILES) {
    resourcefileabsolutepath = $$absolute_path($$resourcefile)
    relativepath_in = $$relative_path($$resourcefileabsolutepath, $$PWD)
    relativepath_out = $$relative_path($$resourcefileabsolutepath, $$OUT_PWD)
    RESOURCE_CONTENT += "<file alias=\"$$relativepath_in\">$$relativepath_out</file>"
}
RESOURCE_CONTENT += \
    "</qresource>" \
    "</RCC>"

write_file($$GENERATED_RESOURCE_FILE, RESOURCE_CONTENT)

I use QtCreator in split side-by-side mode. When switching between views, Qt Creator highlights the currently opened file in the projects list.

Starting in Qt Creator 3.1 it does no longer highlight the file in the project tree (like Foo/bar/QML/qml/main.qml) but the one in the resource file Foo/bar/Resource files/app.qrc/../../Foo/qml/main.qml which is highly distracting, especially since it always expands this huge list of uncategorized files.