Run Android project generated by Maven archetype:generate from IDE by Maven commands

When you create an Android project by Maven e.g. mvn archetype:generate your new Project will be presented in IDE as a Java project, not the Android's one. So you can't run it from IDE as an Android project "out of the box". You should use Maven commands instead:

mvm android:deploy
mvm android:run

By default Maven will deploy your apk on all available deviсes including USB's ones and emulator. So if you want to use only USB devices change related setting in pom.xml of the project.

Why maven doesn't downloads source and javadoc files

When you can not see any source code in your IDE such as Eclipse this most probably happen because your Maven (if you do use Maven) does not downloaded source jar file (e.g. filename-source.jar).

Maven does not downloads a source and javadoc jar files by default.

This option should be added to its settings file in ~/.m2/settings.xml file like this:

<profiles>
<profile>
    <id>downloadSources</id>
    <properties>
        <downloadSources>true</downloadSources>
        <downloadJavadocs>true</downloadJavadocs>           
    </properties>
</profile>
</profiles>

<activeProfiles>
  <activeProfile>downloadSources</activeProfile>
</activeProfiles>

Here is the link about this topic:
http://stackoverflow.com/questions/5780758/maven-always-download-sources-and-javadocs

Debug: how to configure on Mac Eclipse Step Filter to only step through Java code that you've written

If you want to configure Eclipse debugging step filter to only step through Java code that you've written do this (on Mac):

1. Open Preferences window in IDE top menu: Eclipse / Preferences

2. Open Step Filtering settings in Preferences window: Java / Debug / Step Filtering

3. Check packages you want to skip during debugging: 

Android: How to Install Apps using ADB

If you want to install your *.apk of Android application in other way then through IDE as Eclipse use your Terminal and execute command:

adb install path_to_your_application.apk
http://androidcommunity.com/forums/f4/how-to-install-apps-using-adb-4482/