[General Paranoid Android Discussion] jmolinuevo:
Output on my device (Xperia L) CM 11 and Philz touch recovery (CWM 6.0.5.0 based). Similar symptoms as reported by other users, just like to add that some user apps disappear (even if apk is present) because they rely on some Google maps files, and those files got their permissions messed; I tried changing affected files permissions and user apps reappeared. Disappeared system Google apps (like Google+) can't be recovered this way (I suppose they are really missing), so I lately always do clean installs.

gapps-test.txt

------------------------------

drwxr-xr-x 22 root root 0 Aug 29 1970 .

drwxr-xr-x 22 root root 0 Aug 29 1970 ..

drwxr-xr-x 2 root root 0 Aug 29 1970 boot

-rw-r--r-- 1 root root 572 Aug 29 1970 boot.txt

drwxrwx--x 6 system cache 4096 Aug 24 1970 cache

-rwxr-x--- 1 root root 285708 Aug 29 1970 charger

drwxrwx--x 34 system system 4096 Sep 27 20:10 data

drwxr-xr-x 2 root root 0 Aug 29 1970 datadata

-rw-r--r-- 1 root root 3517 Aug 29 1970 default.prop

drwxr-xr-x 10 root root 4640 Aug 29 1970 dev

drwxr-xr-x 2 root root 0 Aug 29 1970 emmc

drwxr-xr-x 2 root root 0 Sep 27 21:09 etc

drwxr-xr-x 2 root root 0 Aug 29 1970 external_sd

-rw-r--r-- 1 root root 11169 Aug 29 1970 file_contexts

-rw-r----- 1 root root 1725 Aug 29 1970 fstab.qcom

-rwxr-x--- 1 root root 191972 Aug 29 1970 init

-rwxr-x--- 1 root root 5577 Aug 29 1970 init.qcom.early_boot.sh

-rwxr-x--- 1 root root 3529 Aug 29 1970 init.qcom.sh

-rwxr-x--- 1 root root 2836 Aug 29 1970 init.qcom.syspart_fixup.sh

-rwxr-x--- 1 root root 3084 Aug 29 1970 init.rc

-rwxr-x--- 1 root root 1752 Aug 29 1970 init.recovery.qcom.rc

drwxr-xr-x 2 root root 0 Aug 29 1970 internal_sd

-rw-r--r-- 1 root root 135804 Jan 1 1970 logo.rle

drwxrwxr-x 5 root system 0 Aug 29 1970 mnt

dr-xr-xr-x 134 root root 0 Jan 1 1970 proc

-rw-r--r-- 1 root root 2161 Aug 29 1970 property_contexts

drwxr-xr-x 2 root root 0 Aug 29 1970 recovery

drwxr-xr-x 3 root root 0 Aug 29 1970 res

drwx------ 2 root root 0 Sep 14 14:30 root

drwxr-x--- 3 root root 0 Aug 29 1970 sbin

drwxr-xr-x 2 root root 0 Aug 29 1970 sd-ext

lrwxrwxrwx 1 root root 16 Aug 29 1970 sdcard -> /storage/sdcard0

-rw-r--r-- 1 root root 660 Aug 29 1970 seapp_contexts

-rw-r--r-- 1 root root 96152 Aug 29 1970 sepolicy

d---r-x--- 3 root sdcard_r 60 Sep 27 21:09 storage

dr-xr-xr-x 13 root root 0 Aug 29 1970 sys

drwxr-xr-x 18 root root 4096 Sep 23 19:02 system

drwxrwxr-x 2 root shell 100 Sep 27 21:09 tmp

-rw-r--r-- 1 root root 10625 Aug 29 1970 ueventd.qcom.rc

-rw-r--r-- 1 root root 7275 Aug 29 1970 ueventd.rc

d---r-x--- 3 root sdcard_r 60 Sep 27 21:09 .

drwxr-xr-x 22 root root 0 Aug 29 1970 ..

drwxrwx--- 26 media_rw media_rw 32768 Sep 27 21:09 sdcard0

/mnt

/mnt/fuse

/mnt/secure

/mnt/secure/staging

/mnt/shell

rootfs on / type rootfs (rw,noatime,nodiratime)

tmpfs on /dev type tmpfs (rw,seclabel,nosuid,noatime,nodiratime,mode=755)

devpts on /dev/pts type devpts (rw,seclabel,noatime,nodiratime,mode=600)

proc on /proc type proc (rw,noatime,nodiratime)

sysfs on /sys type sysfs (rw,seclabel,noatime,nodiratime)

selinuxfs on /sys/fs/selinux type selinuxfs (rw,noatime,nodiratime)

tmpfs on /tmp type tmpfs (rw,seclabel,noatime,nodiratime)

tmpfs on /storage type tmpfs (rw,seclabel,noatime,nodiratime,mode=050,gid=1028)

tmpfs on /mnt/secure type tmpfs (rw,seclabel,noatime,nodiratime,mode=700)

tmpfs on /mnt/fuse type tmpfs (rw,seclabel,noatime,nodiratime,mode=775,gid=1000)

/dev/block/vold/259:0 on /storage/sdcard0 type vfat (rw,dirsync,nosuid,nodev,noexec,noatime,nodiratime,uid=1023,gid=1023,fmask=0007,dmask=0007,allow_utime=0020,codepage=cp437,iocharset=iso8859-1,shortname=mixed,utf8,errors=remount-ro)

/dev/block/platform/msm_sdcc.1/by-name/cache on /cache type ext4 (rw,seclabel,noatime,nodiratime,journal_checksum,journal_async_commit,noauto_da_alloc,errors=panic,data=ordered)

/dev/block/platform/msm_sdcc.1/by-name/userdata on /data type ext4 (rw,seclabel,noatime,nodiratime,data=ordered)

/dev/block/platform/msm_sdcc.1/by-name/system on /system type ext4 (rw,seclabel,noatime,nodiratime,data=ordered)

Filesystem 1K-blocks Used Available Use% Mounted on

tmpfs 430484 128 430356 0% /dev

tmpfs 430484 16 430468 0% /tmp

tmpfs 430484 0 430484 0% /storage

tmpfs 430484 0 430484 0% /mnt/secure

tmpfs 430484 0 430484 0% /mnt/fuse

/dev/block/vold/259:0

4209600 3046720 1162880 72% /storage/sdcard0

/dev/block/platform/msm_sdcc.1/by-name/cache

258184 4544 253640 2% /cache

/dev/block/platform/msm_sdcc.1/by-name/userdata

1647572 1403652 243920 85% /data

/dev/block/platform/msm_sdcc.1/by-name/system

1211576 770872 440704 64% /system