Comment 2 for bug 1401629

Concerning the default directories... I think you should use the XDG_ variables to determine the actual directories, these are usually specified in user-dirs.dirs:
pim@chaos ~ $ cat .config/user-dirs.dirs
# This file is written by xdg-user-dirs-update
# If you want to change or add directories, just edit the line you're
# interested in. All local changes will be retained on the next run
# Format is XDG_xxx_DIR="$HOME/yyy", where yyy is a shell-escaped
# homedir-relative path, or XDG_xxx_DIR="/yyy", where /yyy is an
# absolute path. No other format is supported.
#
XDG_DESKTOP_DIR="$HOME"
XDG_DOWNLOAD_DIR="$HOME/downloads"
XDG_TEMPLATES_DIR="$HOME"
XDG_PUBLICSHARE_DIR="$HOME"
XDG_DOCUMENTS_DIR="$HOME"
XDG_MUSIC_DIR="$HOME/audio"
XDG_PICTURES_DIR="$HOME/pictures"
XDG_VIDEOS_DIR="$HOME/videos"

To test I add the files listed by pantheon-files. I now get the following output:

pim@chaos ~ $ pantheon-files
[_LOG_LEVEL_INFO 22:58:31.275010] Application.vala:153: Files version: 0.2.0
[_LOG_LEVEL_INFO 22:58:31.275099] Application.vala:155: Kernel version: 3.18.0-gentoo
[_LOG_LEVEL_INFO 22:58:31.475058] Application.vala:84: Report any issues/bugs you might find to http://bugs.launchpad.net/pantheon-files
[_LOG_LEVEL_INFO 22:58:31.874597] gof-callwhenready.vala:79: call when ready OK - empty list
[_LOG_LEVEL_FATAL 22:58:31.953428] [GLib] g_variant_ref: assertion 'value->ref_count > 0' failed
[_LOG_LEVEL_FATAL 22:58:31.953585] Files will not function properly.
[_LOG_LEVEL_FATAL 22:58:31.958485] [GLib] g_variant_unref: assertion 'value->ref_count > 0' failed
[_LOG_LEVEL_FATAL 22:58:31.958549] Files will not function properly.
g_dbus_connection_real_closed: Remote peer vanished with error: Underlying GIOStream returned 0 bytes on an async read (g-io-error-quark, 0). Exiting.
Terminated