Gradle configurations do not declare correct inputs/outputs, requiring --rerun-tasks

Support incremental builds by ensuring all tasks correctly specify their inputs and outputs.

This is currently not correctly setup for any shell tasks and all code generation tasks.

Imported from Jira [BEAM-3253](https://issues.apache.org/jira/browse/BEAM-3253). Original Jira may contain additional context.
Reported by: lcwik.

Start by locating the Gradle configurations for shell tasks and code generation tasks, then inspect which inputs and outputs they declare. Confirm the incremental-build behavior and identify the task definitions that require --rerun-tasks. Done means these tasks correctly declare their inputs and outputs so incremental builds work without that flag.

Written by the indexing model from the issue text.