Output of docker version:

Client:
 Version:      1.10.3
 API version:  1.22
 Go version:   go1.5.3
 Git commit:   20f81dd
 Built:        Sat Mar 12 19:18:57 2016
 OS/Arch:      linux/amd64

Server:
 Version:      1.10.3
 API version:  1.22
 Go version:   go1.5.3
 Git commit:   20f81dd
 Built:        Sat Mar 12 19:18:57 2016
 OS/Arch:      linux/amd64

Output of docker info:

Containers: 0
 Running: 0
 Paused: 0
 Stopped: 0
Images: 34
Server Version: 1.10.3
Storage Driver: overlay
 Backing Filesystem: extfs
Execution Driver: native-0.2
Logging Driver: json-file
Plugins: 
 Volume: local
 Network: host bridge null
Kernel Version: 4.4.5-1-ARCH
Operating System: Arch Linux
OSType: linux
Architecture: x86_64
CPUs: 4
Total Memory: 7.533 GiB
Name: arch-t530
ID: 4JN7:HILV:O7E4:VSQX:6T67:BSMT:GQEA:G27K:67TD:UIAF:ZRO5:QUBQ
Username: romansaveljev
Registry: https://index.docker.io/v1/

Additional environment details (AWS, VirtualBox, physical, etc.):

• physical
• Additional files are in https://gist.github.com/RomanSaveljev/55b81155531803d68c52

Steps to reproduce the issue:

1. Grab file-missing.bats from the gist (see above for the link)
2. Install bats (I had it through npm)
3. yes test/file-missing.bats | head -n 100 | xargs node_modules/.bin/bats | tee test.log
4. Study the log

Describe the results you received:
Test failed 24/100 times (see test.log). The reason is that echo 456 >/a in the last layer does not create any modifications to layer.tar. As we can see this is some sort of flakiness in the image builder.

The issue does not manifest, when I split the troubled command into two, like so:

RUN echo 456 >/a
RUN echo def >>/b

100 rounds of the same testcase went fine (see split.log).

I have attached one faulty image (based on alpine) to the same gist for you to examine.

Describe the results you expected:

Both a and b entries exist in the top layer and a contents are 456.

Additional information you deem important (e.g. issue happens only occasionally):

Happens 24/100