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Revert "Reverted changes from PR#1900"

This reverts commit 3769869c339a2d4b753f92617641055adb3e4b16.

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Reverted changes from PR#1900

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Made settings.gradle apply works (and added test)

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Avoid computing relative path when we already know it (because it implies file canonicalization)

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Clean up cached artifact transform outputs on failure or crash.

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Added support for adding directories to `FileStore` instances.

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Javadocs.

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Renamed src/main/groovy to src/main/java in core

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    ./PathNormalisingKeyFileStore.java
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    ./UniquePathKeyFileStore.java
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