Added detection of gems which are not directly under an external subdirectory root (#1841)

* Added proper detection of the list of Gems in the Project Templates
enabled_gems.cmake file

Signed-off-by: lumberyard-employee-dm <56135373+lumberyard-employee-dm@users.noreply.github.com>

* Added a CMake alias target for the Atom Gem and the AtomLyIntegration

Both of those targets just aliases the Atom_AtomBridge gem
Therefore they turn on Atom

Signed-off-by: lumberyard-employee-dm <56135373+lumberyard-employee-dm@users.noreply.github.com>

* Replacing the Atom_AtomBridge gem in the project template with the Atom gem

The Atom gem is just an alias to the Atom_AtomBridge gem

Signed-off-by: lumberyard-employee-dm <56135373+lumberyard-employee-dm@users.noreply.github.com>

* Updated the manifest.py gem gathering logic to recurse through the external subdirecotories locating gem.json files to discover all gems in a subdirectory

Signed-off-by: lumberyard-employee-dm <56135373+lumberyard-employee-dm@users.noreply.github.com>

Templates/DefaultProject/Template/Code/enabled_gems.cmake

@@ -7,7 +7,7 @@
 
 set(ENABLED_GEMS
     ${Name}
-    Atom_AtomBridge
+    Atom
     AudioSystem
     AWSCore
     CameraFramework

Templates/DefaultProject/template.json

@@ -6,7 +6,6 @@
     "license": "What license DefaultProject uses goes here: i.e. https://opensource.org/licenses/MIT",
     "display_name": "Standard",
     "summary": "This template has everything you need to build a full online 3D game or application.",
-    "included_gems": ["Atom","Camera","EMotionFX","UI","Maestro","Input","ImGui"],
     "canonical_tags": [],
     "user_tags": [
         "DefaultProject"