Is it possible for a plugin to change project settings programmatically?

Yes, it is possible. There is no documentation on "how to change settings" in general because each piece of settings is a completely independent API.

You can use JSLibraryManager.getInstance(project).createLibrary() to create a library and .associateWithProject() to associate it with a project. There is no documenation for this API but there is some code that you can use as an example of using this API at https://github.com/JetBrains/intellij-plugins/blob/master/JsTestDriver/src/com/google/jstestdriver/idea/assertFramework/library/JsLibraryHelper.java

Following up on a similar issue,  how can I change the default junit run config via any API? 

Especially I want to add this line: <option name="Make" enabled="false" /> within <method>

```

  <component name="RunManager">

    <configuration default="true" type="JUnit" factoryName="JUnit">

      <module name="" />

      <option name="ALTERNATIVE_JRE_PATH_ENABLED" value="false" />

      <option name="ALTERNATIVE_JRE_PATH" />

      <option name="PACKAGE_NAME" />

      <option name="MAIN_CLASS_NAME" />

      <option name="METHOD_NAME" />

      <option name="TEST_OBJECT" value="class" />

      <option name="VM_PARAMETERS" value="-ea" />

      <option name="PARAMETERS" />

      <option name="WORKING_DIRECTORY" value="file://$PROJECT_DIR$/../../../../../../../../../.." />

      <option name="ENV_VARIABLES" />

      <option name="PASS_PARENT_ENVS" value="true" />

      <option name="TEST_SEARCH_SCOPE">

        <value defaultName="singleModule" />

      </option>

      <envs />

      <patterns />

      <method />

    </configuration>

</component>

```