First shot at starting.

src/main/resources/META-INF/mods.toml

@@ -1,28 +1,55 @@
-modLoader="javafml"
-loaderVersion="[31,)"
-issueTrackerURL="https://github.com/AppliedEnergistics/Applied-Energistics-2/issues"
-showAsResourcePack=false
+# There are several mandatory fields (#mandatory), and many more that are optional (#optional).
+# The overall format is standard TOML format, v0.5.0.
+# Note that there are a couple of TOML lists in this file.
+# Find more information on toml format here:  https://github.com/toml-lang/toml
 
-[[mods]]
-  modId="appliedenergistics2"
-  version="rev7"
-  displayName="Example ModApplied Energistics 2"
-  displayURL="https://ae-mod.info/"
-  logoFile="assets/appliedenergistics2/meta/logo.png"
-  description='''
-  A Mod about Matter, Energy and using them to conquer the world..
-  '''
+# The name of the mod loader type to load - for regular FML @Mod mods it should be javafml
+modLoader="javafml" #mandatory
 
-#  [[dependencies.examplemod]]
-#    modId="forge"
-#    mandatory=true
-#    versionRange="[28,)"
-#    ordering="NONE"
-#    side="BOTH"
-#
-#  [[dependencies.examplemod]]
-#    modId="minecraft"
-#    mandatory=true
-#    versionRange="[1.14.4]"
-#    ordering="NONE"
-#    side="BOTH"
+# A version range to match for said mod loader - for regular FML @Mod it will be the minecraft version (without the 1.)
+loaderVersion="[31,)" #mandatory
+
+# A URL to query for updates for this mod. See the JSON update specification <here>
+#updateJSONURL="" #optional
+
+# A URL to refer people to when problems occur with this mod
+issueTrackerURL="https://github.com/AppliedEnergistics/Applied-Energistics-2/issues" #optional
+
+# A URL for the "homepage" for this mod, displayed in the mod UI
+displayURL="https://github.com/AppliedEnergistics/Applied-Energistics-2" #optional
+
+# A file name (in the root of the mod JAR) containing a logo for display
+logoFile="logo.png"
+
+# A text field displayed in the mod UI
+#credits="Thanks for this example mod goes to Java" #optional
+
+# A text field displayed in the mod UI
+authors="TeamAppliedEnergistics" #optional
+
+# A list of mods - how many allowed here is determined by the individual mod loader
+[[mods]] #mandatory
+
+# The modid of the mod
+modId="appliedenergistics2" #mandatory
+
+# The version number of the mod
+version="${file.jarVersion}" #mandatory
+
+# A display name for the mod
+displayName="Applied Energistics 2" #mandatory
+
+# The description text for the mod (multi line!) (#mandatory)
+description='''
+A Mod about Matter, Energy and using them to conquer the world..
+'''
+
+# A dependency - use the . to indicate dependency for a specific modid. Dependencies are optional.
+[[dependencies.jei]]
+    modId="forge" #mandatory
+    mandatory=true #mandatory
+    versionRange="[31.0.0,)" #mandatory
+    # An ordering relationship for the dependency - BEFORE or AFTER required if the relationship is not mandatory
+    ordering="NONE"
+    # Side this dependency is applied on - BOTH, CLIENT or SERVER
+    side="BOTH"

src/main/resources/assets/appliedenergistics2/META-INF/mods.toml

@@ -1,55 +0,0 @@
-# There are several mandatory fields (#mandatory), and many more that are optional (#optional).
-# The overall format is standard TOML format, v0.5.0.
-# Note that there are a couple of TOML lists in this file.
-# Find more information on toml format here:  https://github.com/toml-lang/toml
-
-# The name of the mod loader type to load - for regular FML @Mod mods it should be javafml
-modLoader="javafml" #mandatory
-
-# A version range to match for said mod loader - for regular FML @Mod it will be the minecraft version (without the 1.)
-loaderVersion="[31,)" #mandatory
-
-# A URL to query for updates for this mod. See the JSON update specification <here>
-#updateJSONURL="" #optional
-
-# A URL to refer people to when problems occur with this mod
-issueTrackerURL="https://github.com/AppliedEnergistics/Applied-Energistics-2/issues" #optional
-
-# A URL for the "homepage" for this mod, displayed in the mod UI
-displayURL="https://github.com/AppliedEnergistics/Applied-Energistics-2" #optional
-
-# A file name (in the root of the mod JAR) containing a logo for display
-#logoFile="examplemod.png" #optional
-
-# A text field displayed in the mod UI
-#credits="Thanks for this example mod goes to Java" #optional
-
-# A text field displayed in the mod UI
-authors="TeamAppliedEnergistics" #optional
-
-# A list of mods - how many allowed here is determined by the individual mod loader
-[[mods]] #mandatory
-
-# The modid of the mod
-modId="appliedenergistics2" #mandatory
-
-# The version number of the mod
-version="${file.jarVersion}" #mandatory
-
-# A display name for the mod
-displayName="Applied Energistics 2" #mandatory
-
-# The description text for the mod (multi line!) (#mandatory)
-description='''
-A Mod about Matter, Energy and using them to conquer the world..
-'''
-
-# A dependency - use the . to indicate dependency for a specific modid. Dependencies are optional.
-[[dependencies.jei]]
-    modId="forge" #mandatory
-    mandatory=true #mandatory
-    versionRange="[31.0.0,)" #mandatory
-    # An ordering relationship for the dependency - BEFORE or AFTER required if the relationship is not mandatory
-    ordering="NONE"
-    # Side this dependency is applied on - BOTH, CLIENT or SERVER
-    side="BOTH"

src/main/resources/mcmod.info

@@ -1,17 +0,0 @@
-[
-    {
-        "modid":"appliedenergistics2",
-        "name":"Applied Energistics 2",
-        "description":"A Mod about Matter, Energy and using them to conquer the world..",
-        "version":"${version}",
-        "mcversion":"${mcversion}",
-        "url":"http://ae2.ae-mod.info",
-        "updateUrl":"",
-        "authorList":[
-         "AlgorithmX2"
-        ],
-        "credits":"AlgorithmX2",
-        "logoFile":"assets/appliedenergistics2/meta/logo.png",
-        "screenshots":[]
-    }
-]