Upstart PID files in home directory?

Question

What are all of these PID files doing in my home directory?

$ ls -1 ~/upstart-*
/home/mark/upstart-dbus-bridge.4885.pid
/home/mark/upstart-file-bridge.4885.pid
/home/mark/upstart-udev-bridge.10317.pid
/home/mark/upstart-udev-bridge.4885.pid
/home/mark/upstart-udev-bridge.6044.pid
/home/mark/upstart-udev-bridge.6406.pid
/home/mark/upstart-udev-bridge.6650.pid

Most are current. If I try to remove them, they will (eventually) come back (albeit with new IDs, etc.).

ps shows the following, for example:

4 S mark      4885  5319  0  80   0 - 27317 poll_s Nov21 ?        00:00:00 /sbin/upstart --user

The same is happening for other users on the same system as well.

Per Jos's comment, the setups of /run / /var/run appear to be correct:

$ mount|grep run
tmpfs on /run type tmpfs (rw,nosuid,noexec,relatime,size=1633648k,mode=755)
tmpfs on /run/lock type tmpfs (rw,nosuid,nodev,noexec,relatime,size=5120k)

$ ll /var/run
lrwxrwxrwx 1 root root 4 Oct 28  2013 /var/run -> /run/

Surely this isn't by design, or that there must be a better place to keep these? As-is, they are not hidden files, nor are they in a hidden directory. This is messy, and result in a longer listing of things I need to look through in what should otherwise be a very clean and organized ~.

I think this started after one of my last upgrades which included systemd. Is this typical, or do I maybe have something else here influencing this that I need to further investigate? (I have gotten a bit lazy here on this system, and haven't performed a clean install for the past few releases - maybe time for a clean install?)

$ cat /etc/lsb-release
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=15.10
DISTRIB_CODENAME=wily
DISTRIB_DESCRIPTION="Ubuntu 15.10"

(This would seem to be something that should be resolved by a simple search, but my Google-fu appears to be failing me with this concern.)

Answer 1

These files are there because several components in your system conform to the XDG Base Directory Specification and expect the environment variable XDG_RUNTIME_DIR to be set. If not set, the user's home directory is used.

pam-systemd is the component that sets XDG_RUNTIME_DIR to /run/user/$UID, where $UID is the effective user id for the user. In your case, pam-systemd has not run or has otherwise misbehaved, that is hard to tell. But you can easily set the XDG_RUNTIME_DIR at boot time yourself, as follows: sudo nano /etc/profile and add the following lines:

XDG_RUNTIME_DIR=/run/user/$UID
export XDG_RUNTIME_DIR

From the next reboot on, the .PID files will no longer clutter your home directory.