diff --git a/abiogenesis.md b/abiogenesis.md
index 0aa64de..b3f7b5f 100644
--- a/abiogenesis.md
+++ b/abiogenesis.md
@@ -8,11 +8,6 @@
   3. The packaging of these molecules into protocells, droplets with membranes
   that maintained an internal chemistry different from that of their
   surroundings
-  4. The origin of self-replicating molecules ([[autocatalytic set]]) that
+  4. The origin of self-replicating molecules ([[autocatalytic-set|autocatalytic set]]) that
   eventually made inheritance possible
-- [[RNA World]]: It's proposed that RNA was the first self-replicating molecule
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[autocatalytic set]: autocatalytic-set "Autocatalytic Set"
-[RNA World]: rna-world "RNA World"
-[//end]: # "Autogenerated link references"
+- [[rna-world|RNA World]]: It's proposed that RNA was the first self-replicating molecule
diff --git a/alternation-of-generations.md b/alternation-of-generations.md
new file mode 100644
index 0000000..22da5ac
--- /dev/null
+++ b/alternation-of-generations.md
@@ -0,0 +1,3 @@
+# Alternation of Generations
+
+- Plants, unlike animals, have [[Sporophytes]] and [[Gametophytes]]
diff --git a/aly.md b/aly.md
index 81379cd..0ed7949 100644
--- a/aly.md
+++ b/aly.md
@@ -4,7 +4,3 @@
 - My [[self]].
 - [[Matrix]] `@aly:scuttlebug.space`
 - [[pull]] [[s5bug]]
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[person]: person "Person"
-[//end]: # "Autogenerated link references"
diff --git a/animalia.md b/animalia.md
new file mode 100644
index 0000000..2f72cc7
--- /dev/null
+++ b/animalia.md
@@ -0,0 +1,2 @@
+# Animalia
+
diff --git a/apicomplexa.md b/apicomplexa.md
index b552712..faff45e 100644
--- a/apicomplexa.md
+++ b/apicomplexa.md
@@ -1,15 +1,9 @@
 # Apicomplexa
 
-- Members of the [[Alveolata]] [[pyhlum]] of the [[SAR Supergroup]]
+- Members of the [[Alveolata]] [[pyhlum]] of the [[sar-supergroup|SAR Supergroup]]
 - Plasmodium Falciparum
   - Causes malaria
 - Toxoplasma Gondii
   - Normal cycle of infection revolves around mice and house cats
   - Makes mice act arrogant around predators to transmit to cats
   - Cat feces carries the parasite, which ends up being transmitted to mice
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Alveolata]: alveolata "Alveolata"
-[SAR Supergroup]: sar-supergroup "SAR Supergroup"
-[//end]: # "Autogenerated link references"
-
diff --git a/archaea.md b/archaea.md
index 8618485..b4b205c 100644
--- a/archaea.md
+++ b/archaea.md
@@ -4,7 +4,7 @@
 - All prokaryotic
 - More closely related to [[eukarya]] than [[bacteria]]
 - Newer findings imply that [[Lokiarchaeota]] are closer than the
-[[TACK Supergroup]] to [[eukarya]]
+[[tack-supergroup|TACK Supergroup]] to [[eukarya]]
 - Vast majority are non-extremophile
 
 ## Taxonomy
@@ -12,7 +12,7 @@
 - [[Archaea]]
   - [[Euryarchaeota]]
   - [[Proteoarchaeota]]
-    - [[TACK Supergroup]]
+    - [[tack-supergroup|TACK Supergroup]]
       - [[Korarchaeota]]
       - TC MRCA
         - [[Thaumarchaeota]]
@@ -20,16 +20,3 @@
     - [[Lokiarchaeota]]
       - Loki1/Loki2
       - Loki3/[[Eukarya]]
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[bacteria]: bacteria "Bacteria"
-[eukarya]: eukarya "Eukarya"
-[Lokiarchaeota]: lokiarchaeota "Lokiarchaeota"
-[TACK Supergroup]: tack-supergroup "TACK Supergroup"
-[Archaea]: archaea "Archaea"
-[Euryarchaeota]: euryarchaeota "Euryarchaeota"
-[Korarchaeota]: korarchaeota "Korarchaeota"
-[Thaumarchaeota]: thaumarchaeota "Thaumarchaeota"
-[Crenarchaeota]: crenarchaeota "Crenarchaeota"
-[Eukarya]: eukarya "Eukarya"
-[//end]: # "Autogenerated link references"
diff --git a/archaeplastida.md b/archaeplastida.md
index 5c4ab7a..b79101c 100644
--- a/archaeplastida.md
+++ b/archaeplastida.md
@@ -1,14 +1,9 @@
 # Archaeplastida
 
-- Original [[eukaryotic]] phototrophe, first to take in a [[cyanobacterium]] as
+- Original [[eukarya|eukaryotic]] phototrophe, first to take in a [[cyanobacteria|cyanobacterium]] as
 an organelle
 - Two lineages:
   - [[Rhodoyhpta]]: Adapted to deeper water by having pigments more absorbant
   of blues
   - [[Viridaeplantae]]: Includes the bulk of the Archaeplastida, including the
   [[Chlorophyta]] and the [[Streptophyta]]
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[eukaryotic]: eukarya "Eukarya"
-[cyanobacterium]: cyanobacteria "Cyanobacteria"
-[//end]: # "Autogenerated link references"
diff --git a/aveao.md b/aveao.md
index 36a3d60..f4395c4 100644
--- a/aveao.md
+++ b/aveao.md
@@ -2,7 +2,3 @@
 
 - A [[person]].
 - Goes by "Ave".
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[person]: person "Person"
-[//end]: # "Autogenerated link references"
diff --git a/bacteria.md b/bacteria.md
index 08a1172..c8b82e5 100644
--- a/bacteria.md
+++ b/bacteria.md
@@ -20,13 +20,3 @@ Gram-negative bacteria form a [[symplesiomorphy]]
       - [[Proteobacteria]]
       - [[Planctobacteria]]
         - [[Chlamydiae]]
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[chemotaxis]: chemotaxis "Chemotaxis"
-[Spirochaeta]: spirochaeta "Spirochaeta"
-[Fermicutes]: fermicutes "Fermicutes"
-[Bacteria]: bacteria "Bacteria"
-[Cyanobacteria]: cyanobacteria "Cyanobacteria"
-[Proteobacteria]: proteobacteria "Proteobacteria"
-[Chlamydiae]: chlamydiae "Chlamydiae"
-[//end]: # "Autogenerated link references"
diff --git a/bedwars.md b/bedwars.md
index 278d2d6..8fde491 100644
--- a/bedwars.md
+++ b/bedwars.md
@@ -2,8 +2,3 @@
 
 - A [[Minecraft]] minigame.
 - Most popular on the [[Hypixel]] network.
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Minecraft]: minecraft "Minecraft"
-[Hypixel]: hypixel "Hypixel"
-[//end]: # "Autogenerated link references"
diff --git a/brown-algae.md b/brown-algae.md
index 90be024..aaf0bbc 100644
--- a/brown-algae.md
+++ b/brown-algae.md
@@ -1,10 +1,5 @@
 # Brown algae
 
-- Members of the [[Heterokonta]] [[phylum]] of the [[SAR Supergroup]]
+- Members of the [[Heterokonta]] [[phylum]] of the [[sar-supergroup|SAR Supergroup]]
 - Macrocystis Pyrifera
   - Giant kelp
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Heterokonta]: heterokonta "Heterokonta"
-[SAR Supergroup]: sar-supergroup "SAR Supergroup"
-[//end]: # "Autogenerated link references"
diff --git a/chalkbot.md b/chalkbot.md
index e5d4168..4179044 100644
--- a/chalkbot.md
+++ b/chalkbot.md
@@ -7,11 +7,5 @@
   - Setting reminders for later dates
   - Managing pronoun roles
   - Having [[shortlinks]]
-- chalkbot aims to use [[Natural Language Processing]] for commands to be
+- chalkbot aims to use [[natural-language-processing|Natural Language Processing]] for commands to be
   ergonomic and multilingual.
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Java]: java "Java"
-[shortlinks]: shortlinks "Shortlinks"
-[Natural Language Processing]: natural-language-processing "Natural Language Processing"
-[//end]: # "Autogenerated link references"
diff --git a/chatchat.md b/chatchat.md
index 19341db..caeaf4a 100644
--- a/chatchat.md
+++ b/chatchat.md
@@ -7,7 +7,3 @@
   [which I've documented on TCRF](https://tcrf.net/ChatChat).
 - I'm working on a [[TypeScript]] reimplementation of the game so that it will
   run without Flash, [open-source on GitDab](https://gitdab.com/s/chatchat).
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[TypeScript]: typescript "TypeScript"
-[//end]: # "Autogenerated link references"
diff --git a/chisel.md b/chisel.md
index d56d2ce..3376abd 100644
--- a/chisel.md
+++ b/chisel.md
@@ -1,7 +1,3 @@
 # Chisel
 
 - A [[Scala]] library for FPGA development.
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Scala]: scala "Scala"
-[//end]: # "Autogenerated link references"
diff --git a/choanoflagellatea.md b/choanoflagellatea.md
new file mode 100644
index 0000000..7a22ba6
--- /dev/null
+++ b/choanoflagellatea.md
@@ -0,0 +1,2 @@
+# Choanoflagellatea
+
diff --git a/chytridiomycota.md b/chytridiomycota.md
new file mode 100644
index 0000000..6d4dca6
--- /dev/null
+++ b/chytridiomycota.md
@@ -0,0 +1,2 @@
+# Chytridiomycota
+
diff --git a/ciliophora.md b/ciliophora.md
index 8a15b8c..f9446ae 100644
--- a/ciliophora.md
+++ b/ciliophora.md
@@ -1,10 +1,5 @@
 # Ciliophora
 
-- Members of the [[Alveolata]] [[pyhlum]] of the [[SAR Supergroup]]
+- Members of the [[Alveolata]] [[pyhlum]] of the [[sar-supergroup|SAR Supergroup]]
 - Have hundreds to thousands of cilia used for feeding and mobility
 - Abundant and diverse in most aquatic habitats
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Alveolata]: alveolata "Alveolata"
-[SAR Supergroup]: sar-supergroup "SAR Supergroup"
-[//end]: # "Autogenerated link references"
diff --git a/cyanobacteria.md b/cyanobacteria.md
index 90fc828..e908361 100644
--- a/cyanobacteria.md
+++ b/cyanobacteria.md
@@ -1,10 +1,6 @@
 # Cyanobacteria
 
-- Responsible for [[The Great Oxygenation]]
+- Responsible for [[the-great-oxygenation|The Great Oxygenation]]
 - [[Spirulina]]: Highly nutritious
 - [[Rivularia]]: Classifies as multi-cellular, as it can regrow its
 photosynthetic filament
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[The Great Oxygenation]: the-great-oxygenation "The Great Oxygenation"
-[//end]: # "Autogenerated link references"
diff --git a/diatoms.md b/diatoms.md
index 2cf2725..1d597e3 100644
--- a/diatoms.md
+++ b/diatoms.md
@@ -1,11 +1,6 @@
 # Diatoms
 
-- Members of the [[Heterokonta]] [[phylum]] of the [[SAR Supergroup]]
+- Members of the [[Heterokonta]] [[phylum]] of the [[sar-supergroup|SAR Supergroup]]
 - Photosynthetic algae, with silica-rich shells
   - When diatomaceous earth is exposed, silica can be harvested from the
   remains of diatoms
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Heterokonta]: heterokonta "Heterokonta"
-[SAR Supergroup]: sar-supergroup "SAR Supergroup"
-[//end]: # "Autogenerated link references"
diff --git a/dinoflagellata.md b/dinoflagellata.md
index 26a9e86..f7770bf 100644
--- a/dinoflagellata.md
+++ b/dinoflagellata.md
@@ -1,10 +1,5 @@
 # Dinoflagellata
 
-- Members of the [[Alveolata]] [[pyhlum]] of the [[SAR Supergroup]]
+- Members of the [[Alveolata]] [[pyhlum]] of the [[sar-supergroup|SAR Supergroup]]
 - Associated with red tides
   - Lingulodinium Polyedrum
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Alveolata]: alveolata "Alveolata"
-[SAR Supergroup]: sar-supergroup "SAR Supergroup"
-[//end]: # "Autogenerated link references"
diff --git a/diplomonadida.md b/diplomonadida.md
index 73e1afb..9fbb168 100644
--- a/diplomonadida.md
+++ b/diplomonadida.md
@@ -4,7 +4,4 @@
 - Giardia Intestinalis
   - Relatively common in wildlife
 
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Metamonada]: metamonada "Metamonada"
-[Excavata]: excavata "Excavata"
-[//end]: # "Autogenerated link references"
+
diff --git a/embryophyta.md b/embryophyta.md
new file mode 100644
index 0000000..b42f3f3
--- /dev/null
+++ b/embryophyta.md
@@ -0,0 +1,11 @@
+# Embryophyta
+
+- Aka land plants
+- [[alternation-of-generations|Alternation of Generations]]
+
+## Taxonomy
+
+- [[Embryophyta]]
+  - Liverworts, Mosses, Hornworts
+  - [[Polysporangiophyta]]
+    - [[Eutracheophyta]]
diff --git a/euglenozoa.md b/euglenozoa.md
index 5eef039..8cf35f9 100644
--- a/euglenozoa.md
+++ b/euglenozoa.md
@@ -9,7 +9,3 @@ Sickness)
   - Transmitted by arthropod vectors
   - Because they're eukaryotic and aerobic, they're hard to target with
   medication
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Excavata]: excavata "Excavata"
-[//end]: # "Autogenerated link references"
diff --git a/eukarya.md b/eukarya.md
index 94f9511..7d59294 100644
--- a/eukarya.md
+++ b/eukarya.md
@@ -7,7 +7,7 @@
   - [[Endomembrane System]]: Documented by [[Christian de Duve]], the
   endomembrane system involves parts of organelles specific to eukaryotic
   organelles, such as the nuclear envelope
-- In eukaryotes, [[mitochondria]] have separate DNA from the nuclear genome,
+- In eukaryotes, [[mitochondrion|mitochondria]] have separate DNA from the nuclear genome,
 which is evidence for [[Endosymbiosis]]
 
 ## Taxonomy
@@ -21,7 +21,7 @@ which is evidence for [[Endosymbiosis]]
           - [[Diplomonadida]]
           - [[Parabasalia]]
     - Diaphoretickes
-      - [[SAR Supergroup]]
+      - [[sar-supergroup|SAR Supergroup]]
         - Rhizaria
           - Cercozoa
           - Retaria
@@ -36,7 +36,7 @@ which is evidence for [[Endosymbiosis]]
           - [[Heterokonta]] (Stramenopiles)
             - [[Diatoms]]
             - [[Oomycota]]
-            - [[Brown algae]]
+            - [[brown-algae|Brown algae]]
       - [[Archaeplastida]]
         - [[Rhodoyhpta]] (red algae)
         - [[Viridiplantae]]
@@ -54,31 +54,5 @@ which is evidence for [[Endosymbiosis]]
         - Nucleariida
         - [[Fungi]]
       - Holozoa
-        - Choanoflagellatea
+        - [[Choanoflagellatea]]
         - [[Animalia]]
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Endosymbiosis]: endosymbiosis "Endosymbiosis"
-[mitochondria]: mitochondrion "mitochondrion"
-[Eukarya]: eukarya "Eukarya"
-[Excavata]: excavata "Excavata"
-[Euglenozoa]: euglenozoa "Euglenozoa"
-[Metamonada]: metamonada "Metamonada"
-[Diplomonadida]: diplomonadida "Diplomonadida"
-[Parabasalia]: parabasalia "Parabasalia"
-[SAR Supergroup]: sar-supergroup "SAR Supergroup"
-[Alveolata]: alveolata "Alveolata"
-[Ciliophora]: ciliophora "Ciliophora"
-[Apicomplexa]: apicomplexa "Apicomplexa"
-[Dinoflagellata]: dinoflagellata "Dinoflagellata"
-[Heterokonta]: heterokonta "Heterokonta"
-[Diatoms]: diatoms "Diatoms"
-[Oomycota]: oomycota "Oomycota"
-[Brown algae]: brown-algae "Brown algae"
-[Archaeplastida]: archaeplastida "Archaeplastida"
-[Unikonta]: unikonta "Unikonta"
-[Amoebozoa]: amoebozoa "Amoebozoa"
-[Eumycetozoa]: eumycetozoa "Eumycetozoa"
-[Opisthokonta]: opisthokonta "Opisthokonta"
-[Fungi]: fungi "Fungi"
-[//end]: # "Autogenerated link references"
diff --git a/eutracheophyta.md b/eutracheophyta.md
new file mode 100644
index 0000000..db85569
--- /dev/null
+++ b/eutracheophyta.md
@@ -0,0 +1,15 @@
+# Eutracheophyta
+
+- True vascular plants
+
+## Taxonomy
+
+- [[Eutracheophyta]]
+  - [[Lycophytes]]
+    - Club Mosses, Spike Mosses, Quillworts
+  - [[Euphyllophytes]]
+    - [[Monilophytes]]
+      - Ferns, Horsetails, Whisk Ferns
+    - [[Spermatophytes]]
+      - [[Gymnosperms]]
+      - [[Angiosperms]]
diff --git a/flancian.md b/flancian.md
index aee7a85..fd53818 100644
--- a/flancian.md
+++ b/flancian.md
@@ -2,8 +2,3 @@
 
 - A [[person]].
 - The creator and maintainer of their [[Agora]].
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[person]: person "Person"
-[Agora]: agora "Agora"
-[//end]: # "Autogenerated link references"
diff --git a/fs2.md b/fs2.md
index 51ccc2e..c420b67 100644
--- a/fs2.md
+++ b/fs2.md
@@ -3,7 +3,3 @@
 - https://fs2.io
 - A [[Scala]] library that allows abstracting data transmission and control
   into a shared concept called a `Stream`.
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Scala]: scala "Scala"
-[//end]: # "Autogenerated link references"
diff --git a/fungi.md b/fungi.md
index d47607a..a965306 100644
--- a/fungi.md
+++ b/fungi.md
@@ -15,8 +15,3 @@ this is not the case
     - Dikarya
       - [[Ascomycota]]
       - [[Basidiomycota]]
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Fungi]: fungi "Fungi"
-[Opisthokonta]: opisthokonta "Opisthokonta"
-[//end]: # "Autogenerated link references"
diff --git a/geologic-timeline.md b/geologic-timeline.md
index 71edeab..29bc0a5 100644
--- a/geologic-timeline.md
+++ b/geologic-timeline.md
@@ -12,21 +12,8 @@
   oxygenation
   - CH₄ (Methane) + 2O₂ → CO₂ + 2H₂O: Methane concentration decreased, while
   Oxygen and CO₂ increased
-  - [[Huronian Glaciation]]
+  - [[huronian-glaciation|Huronian Glaciation]]
   - [[Ediacaran]]
 - [[Phanerozoic]]: 541 MYA to Present
   - Started with a mass-extinction event
   - Divided into [[Paleozoic]], [[Mesozoic]], and [[Cenozoic]]
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Hadean]: hadean "Hadean"
-[Archaean]: archaean "Archaean"
-[Stromatolites]: stromatolites "Stromatolites"
-[Proterozoic]: proterozoic "Proterozoic"
-[Huronian Glaciation]: huronian-glaciation "Huronian Glaciation"
-[Ediacaran]: ediacaran "Ediacaran"
-[Phanerozoic]: phanerozoic "Phanerozoic"
-[Paleozoic]: paleozoic "Paleozoic"
-[Mesozoic]: mesozoic "Mesozoic"
-[Cenozoic]: cenozoic "Cenozoic"
-[//end]: # "Autogenerated link references"
diff --git a/heterokonta.md b/heterokonta.md
index 1af2cc8..5cbe1f6 100644
--- a/heterokonta.md
+++ b/heterokonta.md
@@ -1,7 +1,3 @@
 # Heterokonta
 
-- A [[phylum]] of the [[SAR Supergroup]] with two kinds of flagella
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[SAR Supergroup]: sar-supergroup "SAR Supergroup"
-[//end]: # "Autogenerated link references"
+- A [[phylum]] of the [[sar-supergroup|SAR Supergroup]] with two kinds of flagella
diff --git a/hypixel.md b/hypixel.md
index b70e888..4dc4d06 100644
--- a/hypixel.md
+++ b/hypixel.md
@@ -2,7 +2,3 @@
 
 - https://hypixel.net/
 - A [[Minecraft]] server network.
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Minecraft]: minecraft "Minecraft"
-[//end]: # "Autogenerated link references"
diff --git a/java.md b/java.md
index 295972d..d3bdda9 100644
--- a/java.md
+++ b/java.md
@@ -3,8 +3,3 @@
 - A [[programming language]].
 - Compiled to bytecode that is executed on the [[Java Virtual Machine]].
 - Effectively platform-independent.
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[programming language]: programming-language "Programming Language"
-[Java Virtual Machine]: java-virtual-machine "Java Virtual Machine"
-[//end]: # "Autogenerated link references"
diff --git a/jesyspa.md b/jesyspa.md
index 4cbea5b..833060a 100644
--- a/jesyspa.md
+++ b/jesyspa.md
@@ -1,7 +1,3 @@
 # jesyspa
 
 - A [[person]].
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[person]: person "Person"
-[//end]: # "Autogenerated link references"
diff --git a/journal/2020-10-31.md b/journal/2020-10-31.md
index 15ce813..d1b6ba1 100644
--- a/journal/2020-10-31.md
+++ b/journal/2020-10-31.md
@@ -20,20 +20,7 @@
   of [[Zig]]'s `comptime_float`. The consensus was that, if accurate, it would
   be very useful for expanding [[Zig]]'s floating point datatypes outside of
   just `f16`, `f32`, `f64`, and `f128`.
-- Discovered [[Minecraft, but it's Everywhere At The End Of Time]]. I've
-  figured out that this is some sort of reference to "[[The Caretaker]]," but I
-  don't know what "[[The Caretaker]]" is. I'll have to do more research on it
+- Discovered [[minecraft-but-its-everywhere-at-the-end-of-time|Minecraft, but it's Everywhere At The End Of Time]]. I've
+  figured out that this is some sort of reference to "[[the-caretaker|The Caretaker]]," but I
+  don't know what "[[the-caretaker|The Caretaker]]" is. I'll have to do more research on it
   tomorrow.
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[readme]: ../readme "Aly's digital garden"
-[Ghidra]: ../ghidra "Ghidra"
-[decompilation]: ../decompilation "Decompilation"
-[fs2]: ../fs2 "fs2"
-[sledge]: ../sledge "sledge"
-[Zig]: ../zig "Zig"
-[MinusKelvin]: ../minuskelvin "MinusKelvin"
-[Rust]: ../rust "Rust"
-[Minecraft, but it's Everywhere At The End Of Time]: ../minecraft-but-its-everywhere-at-the-end-of-time "Minecraft, but it's Everywhere At The End Of Time"
-[The Caretaker]: ../the-caretaker "The Caretaker"
-[//end]: # "Autogenerated link references"
diff --git a/journal/2020-11-01.md b/journal/2020-11-01.md
index b3222d1..23de356 100644
--- a/journal/2020-11-01.md
+++ b/journal/2020-11-01.md
@@ -1,13 +1,13 @@
 # 2020-11-01
 
-- Finished listening to [[Minecraft, but it's Everywhere At The End Of Time]].
+- Finished listening to [[minecraft-but-its-everywhere-at-the-end-of-time|Minecraft, but it's Everywhere At The End Of Time]].
   It's made me worry about the effects of dementia and Alzheimer's, whether I
   could contract them, and how much of an effect they would have on me. I'm
   worried about not remembering having created this garden.
 - Implemented `get` and partially implemented `put` on a `HashTableChain`. A
   `HashTableChain` is made up of an array of linked lists, where the array
   index corresponds to some modulo of the hashcode of the key.
-- Played [[Bed Wars]] on [[Hypixel]] in [[Minecraft]] with [[aveao]],
+- Played [[Bedwars]] on [[Hypixel]] in [[Minecraft]] with [[aveao]],
   [[linuxgemini]], and [[lnmds]]. We won with little to no communication;
   amazing team synergy. We plan to play again at some point but with voice
   chat or some other form of unobtrusive communication.
@@ -33,18 +33,3 @@
 - Played [[Bedwars]] again, but with [[SamSeawell]] and [[Sirius902]]. We had
   voice chat at our advantage. We did not lose a single game out of the few we
   played.
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Minecraft, but it's Everywhere At The End Of Time]: ../minecraft-but-its-everywhere-at-the-end-of-time "Minecraft, but it's Everywhere At The End Of Time"
-[Hypixel]: ../hypixel "Hypixel"
-[Minecraft]: ../minecraft "Minecraft"
-[aveao]: ../aveao "Aveao"
-[linuxgemini]: ../linuxgemini "Linuxgemini"
-[lnmds]: ../lnmds "Lnmds"
-[sledge]: ../sledge "sledge"
-[degreetech]: ../degreetech "degreetech"
-[Java]: ../java "Java"
-[Bedwars]: ../bedwars "Bedwars"
-[SamSeawell]: ../samseawell "SamSeawell"
-[Sirius902]: ../sirius902 "Sirius902"
-[//end]: # "Autogenerated link references"
diff --git a/journal/2020-11-02.md b/journal/2020-11-02.md
index d8c54a8..968259a 100644
--- a/journal/2020-11-02.md
+++ b/journal/2020-11-02.md
@@ -11,10 +11,3 @@
   assignments, but I think prior knowledge helped me out a lot.
 - Played [[Hypixel]] again with [[SamSeawell]] and [[Sirius902]] against my
   better judgement.
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[jesyspa]: ../jesyspa "jesyspa"
-[Hypixel]: ../hypixel "Hypixel"
-[SamSeawell]: ../samseawell "SamSeawell"
-[Sirius902]: ../sirius902 "Sirius902"
-[//end]: # "Autogenerated link references"
diff --git a/journal/2020-11-03.md b/journal/2020-11-03.md
index 387ab3a..749786e 100644
--- a/journal/2020-11-03.md
+++ b/journal/2020-11-03.md
@@ -7,10 +7,4 @@
   projects.
 - Having trouble focusing on English work. I'm 3 weeks behind and it's all due
   in 6 days.
-- Decided to watch [[Minecraft, but it's Everywhere At The End Of Time]] again.
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[decompilation]: ../decompilation "Decompilation"
-[Ocarina of Time]: ../the-legend-of-zelda-ocarina-of-time "The Legend of Zelda: Ocarina of Time"
-[Minecraft, but it's Everywhere At The End Of Time]: ../minecraft-but-its-everywhere-at-the-end-of-time "Minecraft, but it's Everywhere At The End Of Time"
-[//end]: # "Autogenerated link references"
+- Decided to watch [[minecraft-but-its-everywhere-at-the-end-of-time|Minecraft, but it's Everywhere At The End Of Time]] again.
diff --git a/journal/2020-11-04.md b/journal/2020-11-04.md
index b34aa9a..aa499ec 100644
--- a/journal/2020-11-04.md
+++ b/journal/2020-11-04.md
@@ -8,9 +8,3 @@
   controller, meant for Phantasy Star Online.
   - Discussed with [[Sirius902]] on how feasible it is to get the ASCII
     GameCube controller working as a normal PC keyboard.
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Flancian]: ../flancian "Flancian"
-[Java]: ../java "Java"
-[Sirius902]: ../sirius902 "Sirius902"
-[//end]: # "Autogenerated link references"
diff --git a/journal/2020-11-05.md b/journal/2020-11-05.md
index a04baa4..45eb506 100644
--- a/journal/2020-11-05.md
+++ b/journal/2020-11-05.md
@@ -3,11 +3,3 @@
 - Worked on an Algebraic Graphs implementation in [[Scala]].
 - Played [[Hypixel]] [[Bedwars]] with [[SamSeawell]] and [[Sirius902]] to
   relieve stress.
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Scala]: ../scala "Scala"
-[Hypixel]: ../hypixel "Hypixel"
-[Bedwars]: ../bedwars "Bedwars"
-[SamSeawell]: ../samseawell "SamSeawell"
-[Sirius902]: ../sirius902 "Sirius902"
-[//end]: # "Autogenerated link references"
diff --git a/journal/2020-11-06.md b/journal/2020-11-06.md
index 4dbeee7..fd42918 100644
--- a/journal/2020-11-06.md
+++ b/journal/2020-11-06.md
@@ -2,8 +2,3 @@
 
 - Happy [[birthday]] to me!
 - Started off my day by playing [[Hypixel]] with [[SamSeawell]].
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Hypixel]: ../hypixel "Hypixel"
-[SamSeawell]: ../samseawell "SamSeawell"
-[//end]: # "Autogenerated link references"
diff --git a/journal/2020-11-07.md b/journal/2020-11-07.md
index 11e9c05..07755a6 100644
--- a/journal/2020-11-07.md
+++ b/journal/2020-11-07.md
@@ -2,8 +2,3 @@
 
 - Took the SAT.
 - Set up Citra to play Ever Oasis with [[SamSeawell]] and [[Sirius902]].
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[SamSeawell]: ../samseawell "SamSeawell"
-[Sirius902]: ../sirius902 "Sirius902"
-[//end]: # "Autogenerated link references"
diff --git a/journal/2020-11-13.md b/journal/2020-11-13.md
index e812e51..cb6dbda 100644
--- a/journal/2020-11-13.md
+++ b/journal/2020-11-13.md
@@ -1,12 +1,5 @@
 # 2020-11-13
 
 - Started working on the ELF reader/writer for [[sledge]].
-- Played [[The Legend of Zelda: The Wind Waker]] with [[Sirius902]] and
+- Played [[the-legend-of-zelda-the-wind-waker|The Legend of Zelda: The Wind Waker]] with [[Sirius902]] and
   [[SamSeawell]].
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[sledge]: ../sledge "sledge"
-[The Legend of Zelda: The Wind Waker]: ../the-legend-of-zelda-the-wind-waker "The Legend of Zelda: The Wind Waker"
-[Sirius902]: ../sirius902 "Sirius902"
-[SamSeawell]: ../samseawell "SamSeawell"
-[//end]: # "Autogenerated link references"
diff --git a/journal/2020-11-29.md b/journal/2020-11-29.md
index b502130..a006ef1 100644
--- a/journal/2020-11-29.md
+++ b/journal/2020-11-29.md
@@ -11,9 +11,3 @@
   [Outwatch](https://outwatch.github.io/?lang=scala) and
   [MathLive](https://mathlive.io/). It exists at
   https://gitlab.com/srnb/complexmap.
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[jesyspa]: ../jesyspa "jesyspa"
-[Chisel]: ../chisel "Chisel"
-[Tenri]: ../tenri "Tenri"
-[//end]: # "Autogenerated link references"
diff --git a/journal/2020-12-03.md b/journal/2020-12-03.md
index 0851582..480819f 100644
--- a/journal/2020-12-03.md
+++ b/journal/2020-12-03.md
@@ -13,10 +13,3 @@
   constructed language.
 - Checked in with [[Flancian]] about my thoughts on the [[Agora]] so far, as
   well as my current personal projects and plans.
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[jesyspa]: ../jesyspa "jesyspa"
-[PETRL]: ../petrl "PETRL"
-[Flancian]: ../flancian "Flancian"
-[Agora]: ../agora "Agora"
-[//end]: # "Autogenerated link references"
diff --git a/journal/2020-12-13.md b/journal/2020-12-13.md
index 7cdd5c4..b0d4909 100644
--- a/journal/2020-12-13.md
+++ b/journal/2020-12-13.md
@@ -2,8 +2,3 @@
 
 - Continued work on my [[Minecraft]] mod that aims to teach functional
   programming concepts via game progression, [[monadmachines]].
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Minecraft]: ../minecraft "Minecraft"
-[monadmachines]: ../monadmachines "monadmachines"
-[//end]: # "Autogenerated link references"
diff --git a/journal/2020-12-27.md b/journal/2020-12-27.md
index ed3ce6c..e8c3c50 100644
--- a/journal/2020-12-27.md
+++ b/journal/2020-12-27.md
@@ -10,13 +10,3 @@
 - Looked into storing times for other users, discovered [[ICU4J]].
 - Looked into [[Natural Language Processing]] software for use in [[chalkbot]].
   - Found [[GrammaticalFramework]].
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Flancian]: ../flancian "Flancian"
-[Agora]: ../agora "Agora"
-[Hoopy the Hoop]: ../hoopy-the-hoop "Hoopy the Hoop"
-[TypeScript]: ../typescript "TypeScript"
-[ChatChat]: ../chatchat "ChatChat"
-[Natural Language Processing]: ../natural-language-processing "Natural Language Processing"
-[chalkbot]: ../chalkbot "chalkbot"
-[//end]: # "Autogenerated link references"
diff --git a/journal/2020-12-28.md b/journal/2020-12-28.md
index 661afad..9283cba 100644
--- a/journal/2020-12-28.md
+++ b/journal/2020-12-28.md
@@ -3,9 +3,3 @@
 - Introduced [[Flancian]] to [[shortlinks]].
 - Worked on documenting my current projects in my garden.
 - Looked into Tweepy for usage in the [[Agora]] [[Twitter]] bot.
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Flancian]: ../flancian "Flancian"
-[shortlinks]: ../shortlinks "Shortlinks"
-[Agora]: ../agora "Agora"
-[//end]: # "Autogenerated link references"
diff --git a/journal/2020-12-31.md b/journal/2020-12-31.md
index dc5346e..1e2976c 100644
--- a/journal/2020-12-31.md
+++ b/journal/2020-12-31.md
@@ -8,7 +8,3 @@
 - Worked on my Unscii to BMFont converter. Fruitless endeavor, the font is much
   too big to be a reasonable size as a BMFont, and I wouldn't even be able to
   get it to work with Webpack.
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[decompilation]: ../decompilation "Decompilation"
-[//end]: # "Autogenerated link references"
diff --git a/journal/2021-01-01.md b/journal/2021-01-01.md
index 005f4f5..0c293b4 100644
--- a/journal/2021-01-01.md
+++ b/journal/2021-01-01.md
@@ -5,7 +5,3 @@
     I gave up and am using C++.
 - [Rant about graphics programming](https://twitter.com/s5bug/status/1345179895341596672).
 - Tried [[Godot]]. A little odd for me, but it'll do what I want thankfully.
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Zig]: ../zig "Zig"
-[//end]: # "Autogenerated link references"
diff --git a/journal/2021-01-03.md b/journal/2021-01-03.md
index 0972a7c..9d907c9 100644
--- a/journal/2021-01-03.md
+++ b/journal/2021-01-03.md
@@ -2,7 +2,3 @@
 
 - Conceptualized an [[OpenGL]] loader in [[Zig]].
 - Looked into solving non-euclidean Rubik's Cubes via [[MagicTile]].
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Zig]: ../zig "Zig"
-[//end]: # "Autogenerated link references"
diff --git a/journal/2021-01-08.md b/journal/2021-01-08.md
index dec8d31..5a17fa3 100644
--- a/journal/2021-01-08.md
+++ b/journal/2021-01-08.md
@@ -1,9 +1,4 @@
 # 2021-01-08
 
-- Played a [[The Legend of Zelda: Ocarina of Time]] [[randomizer]] with
+- Played a [[the-legend-of-zelda-ocarina-of-time|The Legend of Zelda: Ocarina of Time]] [[randomizer]] with
   [[Sirius902]].
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[The Legend of Zelda: Ocarina of Time]: ../the-legend-of-zelda-ocarina-of-time "The Legend of Zelda: Ocarina of Time"
-[Sirius902]: ../sirius902 "Sirius902"
-[//end]: # "Autogenerated link references"
diff --git a/journal/2021-02-10.md b/journal/2021-02-10.md
index 7374ce3..21509a3 100644
--- a/journal/2021-02-10.md
+++ b/journal/2021-02-10.md
@@ -4,8 +4,3 @@
 - Worked more on the Timezone system for [[chalkbot]].
   - [[chalkbot]] now uses [[OpenStreetMap]] to determine the timezone for a
     location.
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[monadmachines]: ../monadmachines "monadmachines"
-[chalkbot]: ../chalkbot "chalkbot"
-[//end]: # "Autogenerated link references"
diff --git a/journal/2021-03-06.md b/journal/2021-03-06.md
index 8f05c8e..9388ebf 100644
--- a/journal/2021-03-06.md
+++ b/journal/2021-03-06.md
@@ -1,7 +1,7 @@
 # 2021-03-06
 
 - Researched into 3d [[pathfinding]] to write an [[AI]] that would play
-  [[Ocarina of Time]] [[randomizer]]s automatically.
+  [[the-legend-of-zelda-ocarina-of-time|Ocarina of Time]] [[randomizer]]s automatically.
   - Look into [[Lazy Theta*]], [[Progressive Octree]]s, and
     [[Edge-Corner Graph]]s:
     https://ascane.github.io/assets/portfolio/pathfinding3d-slides-en.pdf
@@ -14,7 +14,7 @@
 
     —Fig
 - Looked at how to do a [[TAS]]-only trick in
-  [[Ocarina of Time]] to get Fire Arrows in the Max% Child
+  [[the-legend-of-zelda-ocarina-of-time|Ocarina of Time]] to get Fire Arrows in the Max% Child
   run.
   - Max% Child is a [[speedrun]] category where as many items as possible are
     collected before becoming an adult.
@@ -33,7 +33,3 @@
   - Learning how to do [[TAS]] movies in [[BizHawk]].
   - Learning the [[speedrun route]] for Max% Child:
     https://docs.google.com/spreadsheets/d/1yKPI4QPGug0p3Af1O7jZ5vdPUPmxlfQ3FvTSX60kIAY/edit?usp=sharing
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Ocarina of Time]: ../the-legend-of-zelda-ocarina-of-time "The Legend of Zelda: Ocarina of Time"
-[//end]: # "Autogenerated link references"
diff --git a/leyland-james-kirby.md b/leyland-james-kirby.md
index 226338b..70dda8c 100644
--- a/leyland-james-kirby.md
+++ b/leyland-james-kirby.md
@@ -1,9 +1,4 @@
 # Leyland James Kirby
 
 - A [[person]].
-- Creator of [[The Caretaker]].
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[person]: person "Person"
-[The Caretaker]: the-caretaker "The Caretaker"
-[//end]: # "Autogenerated link references"
+- Creator of [[the-caretaker|The Caretaker]].
diff --git a/linuxgemini.md b/linuxgemini.md
index a4acae2..7f4f61a 100644
--- a/linuxgemini.md
+++ b/linuxgemini.md
@@ -1,7 +1,3 @@
 # Linuxgemini
 
 - A [[person]].
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[person]: person "Person"
-[//end]: # "Autogenerated link references"
diff --git a/lnmds.md b/lnmds.md
index 3dcf819..285f819 100644
--- a/lnmds.md
+++ b/lnmds.md
@@ -2,7 +2,3 @@
 
 - A [[person]].
 - Goes by "Luna" or "lun-4".
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[person]: person "Person"
-[//end]: # "Autogenerated link references"
diff --git a/lokiarchaeota.md b/lokiarchaeota.md
index cebd34d..087a6ab 100644
--- a/lokiarchaeota.md
+++ b/lokiarchaeota.md
@@ -1,4 +1,4 @@
 # Lokiarchaeota
 
 - Proposed as a phylum in 2015
-- Closer than the [[TACK Supergroup]] to [[eukarya]]
+- Closer than the [[tack-supergroup|TACK Supergroup]] to [[eukarya]]
diff --git a/mega.md b/mega.md
index d04af2b..e0eef88 100644
--- a/mega.md
+++ b/mega.md
@@ -1,7 +1,3 @@
 # Mega
 
-- [[pull]] [[Molecular Evolutionary Genetics Analysis]]
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Molecular Evolutionary Genetics Analysis]: molecular-evolutionary-genetics-analysis "Molecular Evolutionary Genetics Analysis"
-[//end]: # "Autogenerated link references"
+- [[pull]] [[molecular-evolutionary-genetics-analysis|Molecular Evolutionary Genetics Analysis]]
diff --git a/metamonada.md b/metamonada.md
index 367d3e1..228250c 100644
--- a/metamonada.md
+++ b/metamonada.md
@@ -1,12 +1,5 @@
 # Metamonada
 
-- A [[phylum]] of the [[Excavata]] which lacks [[mitochondria]]
+- A [[phylum]] of the [[Excavata]] which lacks [[mitochondrion|mitochondria]]
   - This means they're adapted to anaerobic environments
 - Includes  [[Diplomonadida]] and [[Parabasalia]]
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Excavata]: excavata "Excavata"
-[mitochondria]: mitochondrion "mitochondrion"
-[Diplomonadida]: diplomonadida "Diplomonadida"
-[Parabasalia]: parabasalia "Parabasalia"
-[//end]: # "Autogenerated link references"
diff --git a/minecraft-but-its-everywhere-at-the-end-of-time.md b/minecraft-but-its-everywhere-at-the-end-of-time.md
index 9eeb66c..7dc7ac2 100644
--- a/minecraft-but-its-everywhere-at-the-end-of-time.md
+++ b/minecraft-but-its-everywhere-at-the-end-of-time.md
@@ -1,15 +1,10 @@
 # Minecraft, but it's Everywhere At The End Of Time
 
 - https://youtu.be/c3gpdZrT0eA
-- This is a rendition of [[The Caretaker]]'s series of albums titled
+- This is a rendition of [[the-caretaker|The Caretaker]]'s series of albums titled
   _Everywhere At The End Of Time_ that achieve the same effect but with the
   [[Minecraft]] soundtrack.
 - YouTube commenter Harvey F. states:
   > I was not the first person to make this comment but 1 in 5 people will know someone with dementia (1). By the age of 65, 1 in 10 of us will develop dementia by the age of 65 (2). The intent of Kirby's project was to simulate the experience of dementia of someone in our current year. This is why the original songs reconstructed by Kirby for his project came out from the 1920's to the 1930's. We know that the most effective way for aiding someone with dementia is to play the songs of their former childhood; "Musical perception, emotion, and memory can survive long after other forms of memory and cognitive function have disappeared" (3).  In the future, this is what some of us will hear, the nostalgic songs of C418, when we cannot think of anything else.
   >
   > (1) alzheimer.ca, (2) alz.org, (3) Music and Dementia: An Overview by Ronald Devere, MD
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[The Caretaker]: the-caretaker "The Caretaker"
-[Minecraft]: minecraft "Minecraft"
-[//end]: # "Autogenerated link references"
diff --git a/minecraft.md b/minecraft.md
index 36bcfa7..a6579c8 100644
--- a/minecraft.md
+++ b/minecraft.md
@@ -1,8 +1,3 @@
 # Minecraft
 
-- A [[video game]] released on May 17, 2009 for [[Java]]-enabled environments.
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[video game]: video-game "Video Game"
-[Java]: java "Java"
-[//end]: # "Autogenerated link references"
+- A [[video-game|video game]] released on May 17, 2009 for [[Java]]-enabled environments.
diff --git a/minuskelvin.md b/minuskelvin.md
index 94529be..ed29100 100644
--- a/minuskelvin.md
+++ b/minuskelvin.md
@@ -2,8 +2,3 @@
 
 - A [[person]].
 - Developer of ColdClear, a Tetris AI written in [[Rust]].
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[person]: person "Person"
-[Rust]: rust "Rust"
-[//end]: # "Autogenerated link references"
diff --git a/mitochondria.md b/mitochondria.md
deleted file mode 100644
index 2b77fe7..0000000
--- a/mitochondria.md
+++ /dev/null
@@ -1,2 +0,0 @@
-# mitochondria
-
diff --git a/mitochondrion.md b/mitochondrion.md
index 2fd9504..9ae867d 100644
--- a/mitochondrion.md
+++ b/mitochondrion.md
@@ -1,2 +1,2 @@
-# mitochondrion
+# Mitochondrion
 
diff --git a/molecular-evolutionary-genetics-analysis.md b/molecular-evolutionary-genetics-analysis.md
index 14ddff9..c2c7e18 100644
--- a/molecular-evolutionary-genetics-analysis.md
+++ b/molecular-evolutionary-genetics-analysis.md
@@ -8,10 +8,6 @@
     - [[CSV]]
   - Can create cladograms
     - Can be output as images
-    - [[Newick Format]]
+    - [[newick-format|Newick Format]]
     - [[CSV]]
 - Does alignment via [[nucleotides]] 
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Newick Format]: newick-format "Newick Format"
-[//end]: # "Autogenerated link references"
diff --git a/monadmachines.md b/monadmachines.md
index c9b655d..3ed7740 100644
--- a/monadmachines.md
+++ b/monadmachines.md
@@ -3,7 +3,3 @@
 - [[Minecraft]] mod that uses a block-building approach to teach functional
   programming.
 - Meant to be usable with no prior programming experience.
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Minecraft]: minecraft "Minecraft"
-[//end]: # "Autogenerated link references"
diff --git a/monilophytes.md b/monilophytes.md
new file mode 100644
index 0000000..03d3b6c
--- /dev/null
+++ b/monilophytes.md
@@ -0,0 +1,2 @@
+# Monilophytes
+
diff --git a/oomycota.md b/oomycota.md
index 15cf0f2..2d2cbd4 100644
--- a/oomycota.md
+++ b/oomycota.md
@@ -1,12 +1,7 @@
 # Oomycota
 
-- Members of the [[Heterokonta]] [[phylum]] of the [[SAR Supergroup]]
+- Members of the [[Heterokonta]] [[phylum]] of the [[sar-supergroup|SAR Supergroup]]
 - Heterotrophic and fungus-like
 - Fish parasites
 - Phytophthora Infestans
   - Cause of Irish Potato Famine
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Heterokonta]: heterokonta "Heterokonta"
-[SAR Supergroup]: sar-supergroup "SAR Supergroup"
-[//end]: # "Autogenerated link references"
diff --git a/opisthokonta.md b/opisthokonta.md
index edeba4c..01a523e 100644
--- a/opisthokonta.md
+++ b/opisthokonta.md
@@ -3,8 +3,3 @@
 - Part of the [[Unikonta]]
 - Named from "rear pole"
 - Having a back-attaching flagellum is rare among [[Eukarya]]
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Unikonta]: unikonta "Unikonta"
-[Eukarya]: eukarya "Eukarya"
-[//end]: # "Autogenerated link references"
diff --git a/parabasalia.md b/parabasalia.md
index 7be07cb..b01cf91 100644
--- a/parabasalia.md
+++ b/parabasalia.md
@@ -9,12 +9,6 @@
     - Mixotricha Paradoxa doesn't produce cellulase
     - Unclear whether the termite actually digests the Mixotricha Paradoxa or
     lets it live
-  - Uses own flagellum as rudders, while [[spirochetes]] power the movement
+  - Uses own flagellum as rudders, while [[spirochaeta|spirochetes]] power the movement
 - Trichomonas Vaginalis
   - Agent of STD in humans
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Metamonada]: metamonada "Metamonada"
-[Excavata]: excavata "Excavata"
-[spirochetes]: spirochaeta "Spirochaeta"
-[//end]: # "Autogenerated link references"
diff --git a/polysporangiophyta.md b/polysporangiophyta.md
new file mode 100644
index 0000000..ba5599d
--- /dev/null
+++ b/polysporangiophyta.md
@@ -0,0 +1,2 @@
+# Polysporangiophyta
+
diff --git a/proteobacteria.md b/proteobacteria.md
index 6556e8c..29731be 100644
--- a/proteobacteria.md
+++ b/proteobacteria.md
@@ -19,7 +19,3 @@
           - βγ
             - Betaproteobacteria
             - Gammaproteobacteria
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Proteobacteria]: proteobacteria "Proteobacteria"
-[//end]: # "Autogenerated link references"
diff --git a/protista.md b/protista.md
index 48951de..32c1ec3 100644
--- a/protista.md
+++ b/protista.md
@@ -3,7 +3,3 @@
 - Not a valid taxon, as it is a [[paraphyly]]
 - Refers to all [[Eukarya]] that are _not_ [[Animalia]], [[Embryophyta]], or
 [[Fungi]]
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Eukarya]: eukarya "Eukarya"
-[//end]: # "Autogenerated link references"
diff --git a/readme.md b/readme.md
index cea86d3..0d4808f 100644
--- a/readme.md
+++ b/readme.md
@@ -6,9 +6,3 @@ This garden is part of an experiment on what being part of a shared digital
 knowledge base entails.
 
 This garden is a part of [[Flancian]]'s [[Agora]].
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Aly]: aly "Aly"
-[Flancian]: flancian "Flancian"
-[Agora]: agora "Agora"
-[//end]: # "Autogenerated link references"
diff --git a/rust.md b/rust.md
index 9fc7152..836f752 100644
--- a/rust.md
+++ b/rust.md
@@ -1,8 +1,4 @@
 # Rust
 
 - https://www.rust-lang.org/
-- A [[programming language]].
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[programming language]: programming-language "Programming Language"
-[//end]: # "Autogenerated link references"
+- A [[programming-language|programming language]].
diff --git a/samseawell.md b/samseawell.md
index 3115ac8..41f47b6 100644
--- a/samseawell.md
+++ b/samseawell.md
@@ -2,7 +2,3 @@
 
 - A [[person]].
 - Goes by "Joe".
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[person]: person "Person"
-[//end]: # "Autogenerated link references"
diff --git a/scala.md b/scala.md
index 43c0875..46f84f5 100644
--- a/scala.md
+++ b/scala.md
@@ -1,10 +1,5 @@
 # Scala
 
 - https://scala-lang.org/
-- A [[programming language]] that mainly runs on the [[Java Virtual Machine]].
+- A [[programming-language|programming language]] that mainly runs on the [[java-virtual-machine|Java Virtual Machine]].
 - Scala can be compiled to JavaScript or via LLVM as well.
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[programming language]: programming-language "Programming Language"
-[Java Virtual Machine]: java-virtual-machine "Java Virtual Machine"
-[//end]: # "Autogenerated link references"
diff --git a/shortlinks.md b/shortlinks.md
index 56af018..a26621f 100644
--- a/shortlinks.md
+++ b/shortlinks.md
@@ -29,7 +29,3 @@
     can be condensed to two characters.
 - Shortlinks should not be URIs themselves.
 - Shortlinks should not obfuscate content, like a traditional link shortener.
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Agora]: agora "Agora"
-[//end]: # "Autogenerated link references"
diff --git a/sirius902.md b/sirius902.md
index 758313e..f9881fd 100644
--- a/sirius902.md
+++ b/sirius902.md
@@ -2,7 +2,3 @@
 
 - A [[person]].
 - Goes by "Christian".
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[person]: person "Person"
-[//end]: # "Autogenerated link references"
diff --git a/sledge.md b/sledge.md
index c264730..621c2f3 100644
--- a/sledge.md
+++ b/sledge.md
@@ -9,9 +9,3 @@
   management like [[Zig]].
 - Meant to have typeclasses like [[Scala]] and operator overloading like
   [[Scala]].
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[fs2]: fs2 "fs2"
-[Zig]: zig "Zig"
-[Scala]: scala "Scala"
-[//end]: # "Autogenerated link references"
diff --git a/spermatophytes.md b/spermatophytes.md
new file mode 100644
index 0000000..de344fe
--- /dev/null
+++ b/spermatophytes.md
@@ -0,0 +1,3 @@
+# Spermatophytes
+
+- [[Heterospory]]
diff --git a/tack-supergroup.md b/tack-supergroup.md
index 76a48d5..12e3770 100644
--- a/tack-supergroup.md
+++ b/tack-supergroup.md
@@ -4,10 +4,3 @@
 - [[Aigarchaeota]]
 - [[Crenarchaeota]]
 - [[Korarchaeota]]
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Thaumarchaeota]: thaumarchaeota "Thaumarchaeota"
-[Aigarchaeota]: aigarchaeota "Aigarchaeota"
-[Crenarchaeota]: crenarchaeota "Crenarchaeota"
-[Korarchaeota]: korarchaeota "Korarchaeota"
-[//end]: # "Autogenerated link references"
diff --git a/tenri.md b/tenri.md
index a501c48..e2d4ab2 100644
--- a/tenri.md
+++ b/tenri.md
@@ -1,7 +1,3 @@
 # Tenri
 
 - A [[person]].
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[person]: person "Person"
-[//end]: # "Autogenerated link references"
diff --git a/the-caretaker.md b/the-caretaker.md
index 4529fc3..1c07e4d 100644
--- a/the-caretaker.md
+++ b/the-caretaker.md
@@ -1,9 +1,5 @@
 # The Caretaker
 
-- A character in a project by [[Leyland James Kirby]].
+- A character in a project by [[leyland-james-kirby|Leyland James Kirby]].
 - A story is told from The Caretaker's perspective about living and dying with
   increasingly severe dementia that becomes Alzheimer's in late life.
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Leyland James Kirby]: leyland-james-kirby "Leyland James Kirby"
-[//end]: # "Autogenerated link references"
diff --git a/the-great-oxygenation.md b/the-great-oxygenation.md
index 0f827a3..182e933 100644
--- a/the-great-oxygenation.md
+++ b/the-great-oxygenation.md
@@ -14,10 +14,3 @@ evolution of [[Cyanobacteria]]
   1. Become a strict anaerobe, and avoid oxygen-containing habitats
   2. Tolerate O₂
      - O₂ toleration can easily lead to aerobic metabolism
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[bacteria]: bacteria "Bacteria"
-[Archaean]: archaean "Archaean"
-[Cyanobacteria]: cyanobacteria "Cyanobacteria"
-[Proterozoic]: proterozoic "Proterozoic"
-[//end]: # "Autogenerated link references"
diff --git a/the-legend-of-zelda-ocarina-of-time.md b/the-legend-of-zelda-ocarina-of-time.md
index 6da26ff..7b2f42b 100644
--- a/the-legend-of-zelda-ocarina-of-time.md
+++ b/the-legend-of-zelda-ocarina-of-time.md
@@ -1,10 +1,5 @@
 # The Legend of Zelda: Ocarina of Time
 
-- A [[video game]] released on November 21, 1998 for the Nintendo 64.
+- A [[video-game|video game]] released on November 21, 1998 for the Nintendo 64.
 - One of the highest rated casual games of all time.
-- Part of [[The Legend of Zelda]] series.
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[video game]: video-game "Video Game"
-[The Legend of Zelda]: the-legend-of-zelda "The Legend of Zelda"
-[//end]: # "Autogenerated link references"
+- Part of [[the-legend-of-zelda|The Legend of Zelda]] series.
diff --git a/the-legend-of-zelda-the-wind-waker.md b/the-legend-of-zelda-the-wind-waker.md
index dd99ad4..fb1aa53 100644
--- a/the-legend-of-zelda-the-wind-waker.md
+++ b/the-legend-of-zelda-the-wind-waker.md
@@ -1,9 +1,4 @@
 # The Legend of Zelda: The Wind Waker
 
-- A [[video game]] released on December 13, 2002 for the Nintendo GameCube.
-- Part of [[The Legend of Zelda]] series.
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[video game]: video-game "Video Game"
-[The Legend of Zelda]: the-legend-of-zelda "The Legend of Zelda"
-[//end]: # "Autogenerated link references"
+- A [[video-game|video game]] released on December 13, 2002 for the Nintendo GameCube.
+- Part of [[the-legend-of-zelda|The Legend of Zelda]] series.
diff --git a/todo.md b/todo.md
index 9aaa2ba..e922122 100644
--- a/todo.md
+++ b/todo.md
@@ -1,20 +1,10 @@
 # Todo
 
-- [ ] Add this garden to the [Agora](https://flancia.org/go/agora)
+- [x] Add this garden to the [Agora](https://flancia.org/go/agora)
 - [ ] Write a [[Ghidra]] plugin to output procedures as individual
   [[MASM Assembly]] files
-- [ ] Finish my contribution of `En_Tg` to the [[Ocarina of Time]]
+- [x] Finish my contribution of `En_Tg` to the [[the-legend-of-zelda-ocarina-of-time|Ocarina of Time]]
   [[decompilation]] project
-- [ ] Draft up a pull request that fixes invalid fields present in
-  `twitter4s`.
 - [ ] Finish my addition of a `HashMap` to `cats-collections`.
 - [ ] Document how I accomplished the Lecture Transcriber written on
   [[2020-11-02]].
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Ghidra]: ghidra "Ghidra"
-[MASM Assembly]: masm-assembly "MASM Assembly"
-[Ocarina of Time]: the-legend-of-zelda-ocarina-of-time "The Legend of Zelda: Ocarina of Time"
-[decompilation]: decompilation "Decompilation"
-[2020-11-02]: journal\2020-11-02 "2020-11-02"
-[//end]: # "Autogenerated link references"
diff --git a/typescript.md b/typescript.md
index 646736c..52894db 100644
--- a/typescript.md
+++ b/typescript.md
@@ -1,8 +1,4 @@
 # TypeScript
 
-- A [[programming language]].
+- A [[programming-language|programming language]].
 - Aims to add [[static typing]] to [[JavaScript]].
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[programming language]: programming-language "Programming Language"
-[//end]: # "Autogenerated link references"
diff --git a/zig.md b/zig.md
index bb38188..fc6e258 100644
--- a/zig.md
+++ b/zig.md
@@ -1,8 +1,4 @@
 # Zig
 
 - https://ziglang.org/
-- A [[programming language]].
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[programming language]: programming-language "Programming Language"
-[//end]: # "Autogenerated link references"
+- A [[programming-language|programming language]].