Here is short version of what you will find when you download the Android source. I will leave out some minor directories and dig deeper into a couple of the important ones. Basically what you will get (based on the current Marshmallow release), in alphabetical order:
BionicThe C-runtime for Android. Note that Android is not using glibc like most Linux distributions. Instead the c-library is called bionic and is based mostly on BSD-derived sources. In this folder you will find the source for the c-library, math and other core runtime libraries.
BootableBoot and startup related code. Some of it is legacy, the fastboot protocol info could be interesting since it is implemented by boot loaders in a number of devices such as the Nexus ones.
BuildThe build system implementation including all the core make file templates. An important file here is the envsetup.sh script that will help you a lot when working with the platform source. Running this script in a shell will enable commands to setup environment variables, build specific modules and grep in source code files.
To ensure devices maintain a high level of quality and offer a consistent user experience, each device must pass tests in the compatibility test suite (CTS). The CTS verifies devices meet a quality standard that ensures apps run reliably and users have a good experience. The test suite to ensure that a build complies with the Android specification.
DalvikThe source code for the implementation of the Dalvik Virtual Machine. The Android runtime (ART) is the heart of Android. It's a fast, ahead-of-time compiled runtime with modern garbage collection designed to scale. Android applications are compiled to Dalvik bytecode and run with ART. This section includes detailed information such as the Dalvik Executable format specification, and design information on the runtime itself.
DevelopmentProjects related to development such as the source code for the sdk and ndk tools. Normally not a folder you touch when working with the platform for a target.
DeviceProduct specific code for different devices. This is the place to find hardware modules for the different Nexus devices, build configurations and more.
Contains source code for all external open source projects such as SQLite, Freetype and webkit.
FrameworksThis folder is essential to Android since it contains the sources for the framework. Here you will find the implementation of key services such as the System Server with the Package- and Activity managers. A lot of the mapping between the java application APIs and the native libraries is also done here.
HardwareHardware related source code such as the Android hardware abstraction layer specification and implementation. This folder also contains the reference radio interface layer (to communicate with the modem side) implementation.
libnativehelperHelper functions for use with JNI.
(Kernel)not part of the default source download but you can get access to this code either by downloading it manually or by adding the repository to the repo tool. Contains the sources for the Android version of the Linux kernel.
Outthe build output will be placed here after you run make. The folder structure is out/target/product/. In the default build for the emulator the output will be placed in out/target/product/generic. This is where you will find the images used by the emulator to start (or to be downloaded and flashed to a device if you are building for a hardware target).
Packagescontains the source code for the default applications such as contacts, calendar, browser.
Prebuiltcontains files that are distributed in binary form for convenience. Examples include the cross compilations toolchains for different development machines.
System - source code files for the core Android system. That is the minimal Linux system that is started before the Dalvik VM and any java based services are enabled. This includes the source code for the init process and the default init.rc script that provide the dynamic configuration of the platform
toolsVarious IDE tools.
Beyond the above you also have the hidden .repo directory that contains the source for the repo utility. It also holds the manifest specifying what git repositories you want to track for this Android source project. If you have your own additions you could automatically track them by adding a local manifest here.
For modifications of the platform framework there are some instructions available in the device/sample folder of the source code tree. That will show you how to add APIs to Android without having to modify the core framework.