chore: simplify and clean up CI workflows (#617)

- Remove redundant Gradle flags, env vars, and unused settings across
all workflows
- Minimize GitHub Actions permissions to least-privilege
- Drop Windows build matrix (JVM tests covered by Linux)
- Simplify CodeQL workflow (remove matrix, unused permissions, stale
triggers)
- Clean up gradle.properties (remove unused KMP settings)

## How Has This Been Tested?
<!-- Have you tested this in a real application? Which scenarios were
tested? -->

## Breaking Changes
—

## Types of changes
- [ ] Bug fix (non-breaking change which fixes an issue)
- [ ] New feature (non-breaking change which adds functionality)
- [ ] Breaking change (fix or feature that would cause existing
functionality to change)
- [ ] Documentation update

## Checklist
- [x] I have read the [MCP
Documentation](https://modelcontextprotocol.io)
- [x] My code follows the repository's style guidelines
- [x] New and existing tests pass locally
- [ ] I have added appropriate error handling
- [ ] I have added or updated documentation as needed

---------

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

gradle.properties

@@ -1,16 +1,10 @@
 org.gradle.jvmargs=-Xmx4g -Dfile.encoding=UTF-8
 org.gradle.parallel=true
 org.gradle.caching=true
-# Dokka
-org.jetbrains.dokka.experimental.gradle.pluginMode=V2Enabled
-org.jetbrains.dokka.experimental.gradle.pluginMode.noWarn=true
 # Kotlin
 kotlin.code.style=official
 kotlin.daemon.jvmargs=-Xmx4G
-# Build JS targets using npm package manager https://kotlinlang.org/docs/js-project-setup.html#npm-dependencies
-kotlin.js.yarn=false
 # MPP
-kotlin.mpp.enableCInteropCommonization=true
 kotlin.native.ignoreDisabledTargets=true
 
 group=io.modelcontextprotocol