Gradle produces incorrect output when a file is removed from a source folder

This is a tragic correctness bug that impacts at least 2.7 and 2.8. To reproduce:

mkdir repro && cd repro
echo "apply plugin: 'java'" > build.gradle
mkdir -p src/main/java
echo "public class T {}" > src/main/java/
gradle jar
unzip -l build/repro.jar
# NOTE: T.class is present in jar
rm src/main/java/
gradle jar
# NOTE: gradle claims jar is "up to date"
unzip -l build/repro.jar
# NOTE: T.class is still present.  Cry deeply.

A clean fixes the issue, but the lack of correctness here is extremely confusing to the user when encountered. Moreover, once a bad artifact is produced, it could easily poison the caches of other tools or build environments that use gradle with the expectation of a properly reproducible build (as happened to me).

Given the severity of this issue, the ease with which it is reproduced, and the sheer volume of potentially impacted users, I think this is an extremely high-severity bug.

I have determined that if is not the only java file in the source folder / resource, then gradle correctly creates a new artifact with the old class file missing. That doesn’t alter the severity of this issue, only the likelihood of others to run into it, IMO.

(also confirmed present on gradle 2.9)

This is a known issue, GRADLE-2579. There are a few workarounds (not great admittedly) mentioned in the issue comments. This is an issue that we are considering prioritizing in a future gradle release.

Thanks for the pointer. I did honestly search for an existing bug, google fail on my part =)