RFR: Gradle cleanup

[Clayton Walker]

I've been doing some development, and came across a few warnings during build.

These are, [Project::task](https://docs.gradle.org/current/javadoc/org/gradle/api/Project.html#task(java.lang.String)) is now deprecated, avoiding Project::mkdir, project::delete and Project::getProjectDir as they cannot work under configuration-cache.

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Commit messages:
 - Fix running with configuration-cache enabled
 - Fix deprecated mkdir call
 - Fix jar inputs
 - Remove use of deprecated task creation method

Changes: https://git.openjdk.org/jextract/pull/283/files
  Webrev: https://webrevs.openjdk.org/?repo=jextract&pr=283&range=00
  Stats: 20 lines in 1 file changed: 5 ins; 0 del; 15 mod
  Patch: https://git.openjdk.org/jextract/pull/283.diff
  Fetch: git fetch https://git.openjdk.org/jextract.git pull/283/head:pull/283

PR: https://git.openjdk.org/jextract/pull/283