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Include Kotlin DSL samples in the plugins doc chapter

See #6424

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Convert user manual to be generated by Asciidoctor only

This change replaces all embedded Docbook syntax from the user manual.

Asciidoctor files are now converted directly to HTML and PDF.

It not only greatly simplifies the user manual generation pipeline, but also it makes it faster.

I did the following for all user manual pages:

- [x] Adjusted links to other manual pages, DSL docs, and Javadocs where necessary.

Fixed a couple dozen broken links at least.

- [x] Convert samples XML from docbook to asciidoctor syntax

- [x] Converted wide tables to a more flexible list-based display

Important contributor differences from now on:

- Users must use a `<file>.adoc#` prefix for all cross-reference links.

This is _required_ to achieve working links in all 3 outputs: multi-page user manual, single-page user manual, and PDF.

- The manual PDF is no longer themed, and no longer has the list of examples links in the TOC.

- File names were changed from camelCased to snake_case to have a crystal clear 1-1 mapping between source to output.

- Section reference verification is now handled by Asciidoctor verbose mode.

- The single-page user manual has the same navigation as the multi-page manual for now.

- [Common Asciidoctor extensions](https://github.com/gradle/dotorg-docs/tree/master/docs-asciidoctor-extensions) are now used by Gradle Guides and the User Manual, however, the the web assets (CSS, JS, etc) are not yet merged.

These extensions are responsible for injecting the navigation and styles.

The header/footer/navigation HTML can now be found under `subprojects/docs/src/main/resources`.

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Fix javaQuickstart sample so that we produce the same output for all Java versions

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Update java (quickstart) samples to use sourceCompatibility 1.7 instead of 1.5

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Upgrade Apache Commons Collections to v3.2.2

Version 3.2.1 has a CVSS 10.0 vulnerability. That's the worst kind of

vulnerability that exists. By merely existing on the classpath, this

library causes the Java serialization parser for the entire JVM process

to go from being a state machine to a turing machine. A turing machine

with an exec() function!

https://web.nvd.nist.gov/view/vuln/detail?vulnId=CVE-2015-8103

https://commons.apache.org/proper/commons-collections/security-reports.html

http://foxglovesecurity.com/2015/11/06/what-do-weblogic-websphere-jboss-jenkins-opennms-and-your-application-have-in-common-this-vulnerability/

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Tabs to spaces +review REVIEW-5060

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Reverted/tweaks some edits to the samples in the interest of readability

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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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use consistent spelling for `customize` throughout docs and codebase

- some minor other spelling improvements along the way

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Use updated repository dsl in some int tests and samples.

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

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