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Improved nested specs example in files chapter

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Explain workaround for Ant default exclusions in files chapter

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Incorporate more feedback into files chapter

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    ./distResources/home.html
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    ./distResources/images/logo.png
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    ./distResources/images/photo.jpg
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    ./distResources/images/plot.eps
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    ./src/main/webapp/products/collaboration.jpg
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Convert examples to tested samples

All the placeholder code examples in working with files are now tested samples

with the introduction of SamplesCopyIntegrationTest and

SamplesFilesMiscIntegrationTest.

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    ./src/main/webapp/index-staging.html
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    ./src/main/webapp/logo.png
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    ./src/main/webapp/products/gradle-staging.html
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    ./src/main/webapp/web.xml
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Intermediate commit to update source tree

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Finish first draft of Working with Files update

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Sample projects should provide root project name as best practice (#3730)

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Remove usage of --no-search-upwards and deprecate

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Fix tests

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Use doLast instead of left shift operator in docs

+review REVIEW-6236

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Use old API methods for task inputs and outputs

Will revert deprecation in next commit.

+review REVIEW-6038

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Revert "Temporarily reverting everything since 810f052813ea0835dc7e9d3eb87bca005815db64 for 3.0-milestone-1 release"

This reverts commit 506f8ce9d6dc1a81e8ff10575c512778ca2f382a.

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Temporarily reverting everything since 810f052813ea0835dc7e9d3eb87bca005815db64 for 3.0-milestone-1 release

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Bind task output files to properties

This change introduces a binding between task properties and output files. Output annotations automatically register property values to the corresponding property name.

The `TaskOutputs` API gained new methods with an `include` prefix that allow more flexible configuration of output properties, including specifying the property name to bind the files to. The old methods have been deprecated.

Properties that were not assigned a property name will be bound to a sequence of pseudo names like `$1`, `$2` etc.

+review REVIEW-6038

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Fix tests

Some leftover fixes for integration tests.

+review REVIEW-6038

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Release notes for filteringCharset on CopySpec

+review REVIEW-5907

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GRADLE-1267 add a filteringCharset property to the copy spec

The copy task (and all the other tasks based on a CopySpec) allow filtering the source files to transform them. But the charset used to read and write the files was always the platform default charset, which causes problem if, for example, the source files are encoded with UTF8 but the platform default charset is another one.

This commit allows specifying a charset to use when filtering the files using `filteringCharset = 'UTF8'` (for example).

Note that the name `filteringCharset` was chosen for this new property as specified in `design-docs/handling-encodings.md`.

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Allow closures passed to LineFilter to remove lines by returning null. - LineFilter no longer implicitly tracks end of file via nullity of transformedLine, but explicitly tracks state (normal, line skip, eof). - Content of copyTestResources/src/two/two.b was unused, so now contains data for line removal integration tests. - Adding an entirely new test file would have affected tests which check which files were copied.

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Tabs to spaces +review REVIEW-5060

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Full proofreading pass on user guide. * Fixed many small typos * Fixed many small grammar issues, requiring small rephrasing * Reworded many phrases to avoid problem with "literal"s being truncated at EOL * Added blank columns to some tables to avoid overwrites * Added newlines to code samples to avoid truncation * Edited all task dependency graphs to use UML "depends on" notation, with arrow from task to depended task, along with a mention of this in the introduction * Added info to "README.md" to describe how to edit graph images * Fixed template link for API references * Ensured text uses "left double quote" and "right double quote" where appropriate * Made a handful of small actual content changes to emphasize points not fully covered * Changed some "p" elements to "para" * Changed some "thread" elements to "thead"

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Doc : improved Copy task VS copy() method chapter

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Fixed some problems with samples tests after the changes in the implicit tasks and dependency insight task.

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GRADLE-2135: warn about using zipTree() with non existing zip file

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    ./src/main/assets.zip
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Update userguide and samples with information about using from task / from task.outputs

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Turn on deprecation checking for integration tests by default: disabled in a few cases - use GradleDistributionExecuter.ignoreDeprecationWarnings() in cases where warnings are still emitted in tests - Ignore idea.ConfigurationHooksTest.triggersBeforeAndWhenConfigurationHooks, since this test fails due to a bug - A few other tests still failing

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Renamed subprojects/gradle-(.+) to subprojects/$1

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