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

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Merged internal `ResourceNotFoundException` into public `MissingResourceException`.

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Added a resource location to `ResourceException` and subtypes. Use `ResourceException` instead of `IOException` when something goes wrong fetching a resource's content or meta-data.

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If an explicit settings file has been set, error if it does not exist.

+review REVIEW-5411

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Fixes for class loader caching.

We weren't distinguishing between runtime loaders for the different passes of a build script. This meant that if a script contained a `buildscript {}` block, then we'd cache the loader for the first pass. We'd then run the second path with the same loader id, and a different effective loader. This would evict the first pass loader, which would then be evicted on the next build etc. The build script class loader ids now indicate the phase, allowing both loaders to be cached.

We weren't releasing loaders when scripts disappeared. We now explicitly “remove” runtime script loaders if the script is empty. This also required giving empty and missing scripts) identity, in terms of the file that should have contained the script.

Reworking the testing infrastructure raised these issues, and some other bad assumptions that the tests were incorrectly attempting to assert.

+review REVIEW-5411

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Revert "Message for incubating execution mode is not shown if the mode is explicitly configured (e.g. gradle.properties)."

This reverts commit 7fa641429cdd04a00f8bdf3f6364909fbd32a5ae.

It didn't work for the daemon execution and I wasn't happy with the implementation, too.

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Revert "Message for incubating execution mode is not shown if the mode is explicitly configured (e.g. gradle.properties)."

This reverts commit 7fa641429cdd04a00f8bdf3f6364909fbd32a5ae.

It didn't work for the daemon execution and I wasn't happy with the implementation, too.

(cherry picked from commit d21b4bc)

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Message for incubating execution mode is not shown if the mode is explicitly configured (e.g. gradle.properties).

1. The use case is that organisations may roll out incubating mode to all projects and don't want to confuse the end users (e.g. fear about the features that may be perceived incomplete, confusing request for feedback in the incubating message). So, if the incubating mode is explicitly configured in the gradle properties, we assume that the user knows what he is doing and need not be reminded about the incubating nature of the feature. (while writing this commit message it just occurred to me that this should be in the spec)

2. The implementation is not quite pretty, looking for suggestions on how to improve it.

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    ./GradleProperties.java
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Remove the deprecated methods from StartParameter.

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Moved logic for determining the build layout when settings file has been provided on the command line so that it lives behind BuildLayoutFactory, and removed EmbeddedScriptSettingsFinder.

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    ./BuildLayoutConfiguration.java
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Changed BuildLayout to extend SettingsLocation, and changed DefaultSettingsFinder to simply pass through the BuildLayout.

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Roll back using gradle-wrapper.properties to find root directory. Doesn't make any sense.

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GRADLE-1765 - Merged the logic for finding the root directory from WrapperExecuter and various SettingsFinderStrategy impls into a single BuildLayoutFactory. - Searching for the root directory now stops at the first directory that contains a settings.gradle or a gradle/wrapper/gradle-wrapper.properties. - Fixed for broken unit test.

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    ./BuildLayoutFactory.java
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