giant freakin documentation and reorganization pass, it also uses cmake because all the building was getting too complicated for shell scripts

pak/upgrades/agility.mmd

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+---
+title: Agility Upgrades
+theme: base
+themeVariables:
+    primaryColor: "#00aa00"
+---
+flowchart LR
+    speed1@{label: "Speedier Seagull"}
+    speed2@{label: "Greased Wings"}
+
+    theft_chance1@{label: "Swooping Techniques"}
+    theft_chance2@{label: "The Element of Surprise"}
+
+    passive_shinies_income1@{label: "Get On The Floor"}
+    passive_shinies_income2@{label: "Open The Door"}
+    passive_shinies_income3@{label: "Walk Like A Dinosaur"}
+
+    speed1-->speed2
+    theft_chance1-->speed1
+    theft_chance1-->theft_chance2
+
+    theft_chance1-->passive_shinies_income1
+                 -->passive_shinies_income2
+                 -->passive_shinies_income3

pak/upgrades/instinct.mmd

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+---
+title: Instinct Upgrades
+theme: base
+themeVariables:
+    primaryColor: "#aa00ff"
+---
+flowchart LR
+    xp_bonus1@{label: "Stop and Smell"};
+    xp_bonus2@{label: "Ponder and Deliberate"};
+    xp_bonus3@{label: "Plan and Strategize"};
+
+    theft_results1@{label: "Go For The Pockets"};
+    theft_results2@{label: "Use The Winds"};
+
+    passive_food_income1@{label: "Gone Fishin'"};
+    passive_food_income2@{label: "Gone Farmin'"};
+    passive_food_income3@{label: "Gone Clickin'"};
+    passive_food_income4@{label: "Gone Agin'"};
+    passive_food_income5@{label: "Gone Minin'"};
+    passive_food_income6@{label: "Gone Factorin'"};
+    passive_food_income7@{label: "Gone Bankin'"};
+
+    passive_food_income1-->passive_food_income2
+                        -->passive_food_income3
+                        -->passive_food_income4
+                        -->passive_food_income5
+                        -->passive_food_income6
+                        -->passive_food_income7;
+    
+    xp_bonus1-->xp_bonus2
+             -->xp_bonus3;
+
+    theft_results1-->theft_results2
+                  -->xp_bonus3;

pak/upgrades/leadership.mmd

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+---
+title: Leadership Upgrades
+theme: base
+themeVariables:
+    primaryColor: "#ffaa00"
+---
+flowchart LR
+    offline_gen@{label: "Tireless Colony"}
+    offline_gen_bonus1@{label: "Swoop Where He's Unprepared"}
+    offline_gen_bonus2@{label: "Fly Where You're Unexpected"}
+
+    recruit_chance1@{label: "Squawk Softly"}
+    recruit_chance2@{label: "Wink"}
+    recruit_chance3@{label: "Sea Tzu's Art of Swoop"}
+
+    recruit_chance1-->recruit_chance2
+    recruit_chance2-->recruit_chance3
+
+    recruit_chance3-->offline_gen_bonus1
+    offline_gen---->offline_gen_bonus1
+    offline_gen_bonus1-->offline_gen_bonus2
+