My comments.

files/variables.js

@@ -1,6 +1,8 @@
 // Now holds only variables
 
-// Items
+// To allow a variable to be read/wrote from across files you must begin them with "global.variablename"
+
+// Items and related stats
 global.supplyList = [ // Supplies: chems, aid
     {name: "Food", description: "Misc foods", cost: 1, weight: 0},
     {name: "Stimpak", description: "A Stimpak syringe, heals 25  HP", cost: 5, weight: 0.5},
@@ -39,6 +41,7 @@ global.equipmentList = [ // Equipment: weapons, armor, tools
     {name: "Fists (Unarmed)", description: "Unarmed combat, does 5 bash damage", type: "weapon", value: "5", unit: "bash", cost: 5, weight: 1},
 ];
 
+// List of possible achievements you can gain (Currently not used in game)
 global.achievements = [
     // POI/Faction Destroy
     {name: "Dishonorable Discharge", description: "Deactivate MODUS at the Whitespring", unlocked: false},
@@ -96,8 +99,8 @@ global.inventory = [  // Inventory of player, holds all items
     equipmentList[27],
     equipmentList[25],
 ]
-global.equippedWeapon = equipmentList[27];
-global.equippedArmor = equipmentList[25];
+global.equippedWeapon = equipmentList[27]; // Players currently equipped weapon
+global.equippedArmor = equipmentList[25];  // PLayers currently equipped armor
 
 // Game Mechanics
 global.walkRate = 0;  // Units the player walks per day, affects foodRateCalc and radPointsCalc