Add Step-02 example agent: add a shell execution tool (#966)

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## Motivation and Context
Second step of the code agent example.

## Breaking Changes
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---

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

#### Checklist
- [x] The pull request has a description of the proposed change
- [x] I read the [Contributing
Guidelines](https://github.com/JetBrains/koog/blob/main/CONTRIBUTING.md)
before opening the pull request
- [x] The pull request uses **`develop`** as the base branch
- [ ] Tests for the changes have been added
- [x] All new and existing tests passed

##### Additional steps for pull requests adding a new feature
- [ ] An issue describing the proposed change exists
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- [ ] The change was discussed and approved in the issue
- [ ] Docs have been added / updated

---------

Co-authored-by: Bruno Lannoo <BLannoo@users.noreply.github.com>

Author: denis-domanskii

examples/code-agent/step-02-add-execution-tool/Module.md

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+# Module Code Agent (Step 2)
+
+Code Agent example.

examples/code-agent/step-02-add-execution-tool/README.md

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+# Code Agent - Step 01: Minimal Agent
+
+> Code from the blog post: [Building AI Agents in Kotlin – Part 2: A Deeper Dive Into Tools]()
+
+A minimal code agent with three tools that can navigate codebases and make targeted changes.
+
+## Prerequisites
+
+- Java 17+
+- OpenAI API key
+
+## Setup
+
+```bash
+export OPENAI_API_KEY=your_openai_key
+```
+
+## Run
+
+Navigate to this example:
+```
+cd examples/code-agent/step-01-minimal-agent
+```
+
+Run the agent on any project:
+```
+./gradlew run --args="/absolute/path/to/project 'Task description'"
+```
+
+Example:
+```
+./gradlew run --args="/Users/yourname/my-project 'Add error handling'"
+```

examples/code-agent/step-02-add-execution-tool/build.gradle.kts

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+plugins {
+    alias(libs.plugins.kotlin.jvm)
+    alias(libs.plugins.shadow)
+    application
+}
+
+application.mainClass.set("ai.koog.agents.examples.codeagent.step02.MainKt")
+
+dependencies {
+    implementation("ai.koog:koog-agents")
+    implementation(libs.kotlinx.coroutines.core)
+    implementation(libs.logback.classic)
+}
+
+tasks.test {
+    useJUnitPlatform()
+}
+
+tasks.shadowJar {
+    archiveBaseName.set("code-agent")
+    mergeServiceFiles()
+}
+
+tasks.named<JavaExec>("run") {
+    standardInput = System.`in`
+}

examples/code-agent/step-02-add-execution-tool/gradle.properties

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+#Kotlin
+kotlin.code.style=official
+kotlin.daemon.jvmargs=-Xmx4096M
+
+#Gradle
+org.gradle.jvmargs=-Xmx4096M -Dfile.encoding=UTF-8
+org.gradle.parallel=true
+org.gradle.caching=true

examples/code-agent/step-02-add-execution-tool/gradle/libs.versions.toml

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+[versions]
+kotlin = "2.2.20"
+kotlinx-coroutines = "1.10.2"
+kotlinx-serialization = "1.8.1"
+logback = "1.5.13"
+shadow = "9.1.0"
+
+[libraries]
+kotlinx-coroutines-core = { module = "org.jetbrains.kotlinx:kotlinx-coroutines-core", version.ref = "kotlinx-coroutines" }
+logback-classic = { module = "ch.qos.logback:logback-classic", version.ref = "logback" }
+
+[plugins]
+kotlin-jvm = { id = "org.jetbrains.kotlin.jvm", version.ref = "kotlin" }
+kotlin-serialization = { id = "org.jetbrains.kotlin.plugin.serialization", version.ref = "kotlin" }
+shadow = { id = "com.gradleup.shadow", version.ref = "shadow" }

examples/code-agent/step-02-add-execution-tool/gradle/wrapper/gradle-wrapper.jar

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+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.14-bin.zip
+networkTimeout=10000
+validateDistributionUrl=true
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists