Missing files in rootfs when adding links /bin ->/usr/bin and /lib -> /usr/lib in recipe base-files

["Jan Lindåker" <jan.lindaker@axis.com>]

I'm trying to 

When changing package base-files, so that the /bin directory is soft linked to /usr/bin and the /lib directory is soft linked to /usr/lib, the resulting image/rootfs directory structure is missing a lot of files, most of which are unrelated to any of the  directories mentioned above. E.g. file://etc/fstab is missing. When inspecting the base-files .rpm it contains the file structure​ that is expected. For some reason the package install order changes when building rootfs when the links from /lib and /usr are present.

I know too little about Yocto/kernel image building to be able to debug this effectively, since there is no errors reported and the build process is quite complex. Any solutions or help with where to continue my investigations would be highly appreciated.

Actions to reproduce:
I first detected the problem in an adaptation of Yocto, but I have reproduced it in the project described in the quick start: http://www.yoctoproject.org/docs/1.8/yocto-project-qs/yocto-project-qs.html

1. Set up a new Yocto project as described in the link above
2. Set up a new layer with a .bbappendfile as follows

-- ../recepies-linkdir/base-files/base-files_%.bbappend -------------------
dirs755_remove = "/bin /lib"

do_install_extra_links() {
    ln -srvf ${D}/usr/bin ${D}/bin
    ln -srvf ${D}/usr/lib ${D}/lib
}

addtask install_extra_links after do_install before do_populate_sysroot do_packag

-- ../meta-linkdir/conf/layer.conf ----------------------------------------
# We have a conf and classes directory, add to BBPATH 
BBPATH =. "${LAYERDIR}:" 
# We have a packages directory, add to BBFILES 
BBFILES += "${LAYERDIR}/recipes-*/*/*.bb \ 
            ${LAYERDIR}/recipes-*/*/*.bbappend"
            
BBFILE_COLLECTIONS += "linkdir" 
BBFILE_PATTERN_linkdir := "^${LAYERDIR}/" 
BBFILE_PRIORITY_linkdir := "6"

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

3. Build the software
$ bitbake core-image-sato

4. Inspect the .rpm
rpm -lvpq ./tmp/work/qemux86-poky-linux/base-files/3.0.14-r89/deploy-rpms/qemux86/base-files-dev-3.0.14-r89.qemux86.rpm
Note that: /bin -> /usr/bin, /lib -> /user/lib and that /etc/fstab is present

5. Save the generated file-strucutre
$ pushd ./tmp/work/qemux86-poky-linux/core-image-sato/1.0-r0/rootfs
$ LC_ALL=C find . -exec "stat -c '%N' {} \;" > /tmp/yocto_link_fs.txt
$ popd

6. Save the build log from rootfs build
$ cp .tmp/work/qemux86-poky-linux/core-image-sato/1.0-r0/temp/log.do_rootfs /tmp/log.do_rootfs.link

7. To be able to compare with the original filesystem, disable the changes in the .bb-append file, i.e. edit it to look like this:
-- ../recepies-linkdir/base-files/base-files_%.bbappend -------------------
# dirs755_remove = "/bin /lib"

do_install_extra_links() {
    ln -srvf ${D}/usr/bin ${D}/bin
    ln -srvf ${D}/usr/lib ${D}/lib
}

# addtask install_extra_links after do_install before do_populate_sysroot do_packag

8. Rebuild the project
$ bitbake -c cleanall base-files
$ bitbake core-image-sato

9. Inspect the .rpm
rpm -lvpq ./tmp/work/qemux86-poky-linux/base-files/3.0.14-r89/deploy-rpms/qemux86/base-files-dev-3.0.14-r89.qemux86.rpm
Note that: /bin and /lib are normal directories and that /etc/fstab is present

10. Save the generated file-strucutre
$ pushd ./tmp/work/qemux86-poky-linux/core-image-sato/1.0-r0/rootfs
$ LC_ALL=C find . -exec "stat -c '%N' {} \;" > /tmp/yocto_orig_fs.txt
$ popd

11. Save the build log from rootfs build
$ cp .tmp/work/qemux86-poky-linux/core-image-sato/1.0-r0/temp/log.do_rootfs /tmp/log.do_rootfs.orig

12. Compare the difference and note that files are exclusively missing from the build where the soft-links where added.
$  diff /tmp/yocto_orig_fs.txt /tmp/yocto_links_fs.txt
2d1
< './proc'
16d14
< './usr/share/info'
3643d3640
< './usr/share/dict'
5068,5070d5064
< './usr/share/dbus-1/interfaces/org.freedesktop.ConsoleKit.Seat.xml'
< './usr/share/dbus-1/interfaces/org.freedesktop.ConsoleKit.Session.xml'
< './usr/share/dbus-1/interfaces/org.freedesktop.ConsoleKit.Manager.xml'
5075d5068
< './usr/share/dbus-1/system-services/org.freedesktop.ConsoleKit.service'
5382d5374
< './usr/share/man'
5386d5377
< './usr/src'
5488d5478
< './usr/bin/ck-launch-session'
5603d5592
< './usr/bin/ck-list-sessions'
5674d5662
< './usr/bin/ck-history'
5708d5695
< './usr/sbin/ck-log-system-restart'
5710d5696
< './usr/sbin/ck-log-system-stop'
5758d5743
< './usr/sbin/ck-log-system-start'
5771d5755
< './usr/sbin/console-kit-daemon'
6119d6102
< './usr/lib/libck-connector.so.0.0.0'
6287d6269
< './usr/lib/libck-connector.so.0' -> 'libck-connector.so.0.0.0'
7570,7571d7551
< './usr/lib/ConsoleKit/scripts/ck-system-stop'
< './usr/lib/ConsoleKit/scripts/ck-system-restart'
7597,7599d7576
< './usr/lib/consolekit/ck-get-x11-display-device'
< './usr/lib/consolekit/ck-get-x11-server-pid'
< './usr/lib/consolekit/ck-collect-session-info'
7739,7740d7715
< './dev'
< './run'
7812,7813d7786
< './home'
< './home/root'
7818d7790
< './etc/nsswitch.conf'
7823d7794
< './etc/default/usbd'
7910d7880
< './etc/fstab'
7936d7905
< './etc/hostname'
7983d7951
< './etc/motd'
8020d7987
< './etc/profile'
8086d8052
< './etc/mtab' -> '/proc/mounts'
8098d8063
< './etc/filesystems'
8138d8102
< './etc/issue.net'
8163d8126
< './etc/host.conf'
8227d8189
< './etc/dbus-1/system.d/ConsoleKit.conf'
8434d8395
< './etc/issue'
8446d8406
< './etc/ConsoleKit/seats.d/00-primary.seat'
8460,8465d8419
< './etc/inputrc'
< './etc/skel'
< './etc/skel/.bashrc'
< './etc/skel/.profile'
< './tmp'
< './sys'
8533d8486
< './media'
8535d8487
< './var/lock' -> '../run/lock'
8544,8549c8496
< './var/volatile'
< './var/run' -> '../run'
< './var/tmp' -> 'volatile/tmp'
< './var/backups'
< './var/local'
< './var/log' -> 'volatile/log'
---
> './var/log'
8562d8508
< './var/lib/misc'

13. Note that the package install order (for some strange rason) has changed by comparing the rootfs-logs
diff /tmp/log.do_rootfs
.tmp/work/q1775-poky-linux/axis-image-cvp/1.0-r0/temp/log.do_rootfs


Conclusion/Expected results
==========

The resulting file-system is not the intended with many missing files (regardless of if there are bugs in Yocto, the packages, or that the change made is not possible to do for technical reasons). Regardless of the root cause of the bad file-system, no  error messages are presented by Yocto or the package installation process. It is unclear for me whether the latter depends on bugs in the rpm packaging system, the packages or that Yocto eats the error reporting from rpm.

/Best regards Jan