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Please make sure you have read the entire readme before you install or edit either of the two Anodyne files. This tutorial only covers how to edit the files, because I thought some people might like to have pictures showing exactly what to change.
I would be very surprised if you have the exact same preferences for everything that I do, and there is probably at least one thing included in this by default that you don't like. Maybe you want your engineering icon after all the terrarium icons. Maybe you use a different autonamer. Maybe you have another twenty agents that you want to inject into almost every world that you make. Here's how to make that happen. Open up the .cos file you want to edit - I recommend CAOS Tool, or at least Notepad++, but a normal simple text editor (Notepad, gedit, etc) will work as well.
Making changes is not hard, even if you don't know any CAOS! However, because these files have permanent effects on new worlds, please test your changes on a temporary new world. I highly recommend making both an undocked and a docked test just to make sure that no errors pop up and nothing happens that you don't want to happen.
For the Anodyne part one file
If you don't want something to be removed, look for the line that says 'kill off ____' where ____ is the thing you want to keep. Either comment out the three lines following it (the ones that say enum ___, kill targ, next) by putting a * in front of them, or delete them.
(These demonstration images show commenting out because it is less destructive, but the effect is the same either way.)

This example shows how to keep the file from deleting the knowledge stones from your worlds.
If you want to have something else automatically removed, then add three lines in the section full of 'kill off ___' lines. If the agent is present in DS, do this before the line that says 'doif gmap 1538 3272 ne -1'. If the agent is present only in C3, it is best to put it AFTER the line that says 'doif gmap 1538 3272 ne -1'. The three lines you want to add are:
enum x y z
kill targ
next
Here x y z is the classifier number of the object you want to kill. If you don't know it, open up a world, hit ctrl-shift-t, and hover the hand over the object. Three numbers will come up on your screen. Record those three numbers and plug them into the 'x y z' exactly as they appeared in the game.

In this example, I added the classifier of the DS elevator buttons (maybe if you wanted to raze everything and use Elevines instead?).
If you don't want to turn off the Empathetic Vendor's hearing ability, either delete or comment out these lines by putting a * in front of them:
enum 2 23 3
setv ov00 0
part 1
pose 0
next

If you want to have the hand be called something other than "hand", change the line that says 'hand "hand"', to replace the "hand" with whatever you want the hand to be called. (Don't forget the quotes.)

You probably didn't need this image, but it's here for the sake of completeness.
If you want your room icons to be in a different order, go down to the part that says 'move camera to hallway' and then has a bunch of lines like this: cmra 6143 8998 0. The 'cmra 6143 8998 0' part is telling the game where to point the camera, so to change the order of your icons, you just have to change the order of those lines. I recommend changing the comments as well (the lines starting with **) to describe the new order, to keep from getting yourself confused. For example, if you wanted to have the Workshop icon be second, not the hallway icon, you would find the cmra line for the Workshop (cmra 4611 9039 0) and put it where the cmra line for the hallway is (cmra 2469 9046 0). Then you would take the cmra line for the hallway, and put it where the cmra line for the Workshop used to be. It is possible to change things around so that C3 icons can come before DS icons, as well.

This shows the above example.
For the Anodyne part two file
This file is actually easier to change than part one, woo! It also has the potential to cause errors. Be careful when modifying it!
Keep in mind that agents do not need to be in alphabetical order; I just did that to make things easier for me.
If you don't want to automatically add one of the agents in the file to your worlds (or you don't have it, etc), all you have to do is either comment out (add * before it) or take out the line that says 'sets va01 ___' (where ___ is the name of the agent), and the same to the 'elif ov00 eq ___' line just before it. You can also remove the comment (the line starting with **) if you want. Then, you must change all the following 'elif ov00 eq ___' lines following it to subtract one from whatever the 'eq ___' number is for every agent before that line that you removed. For example, if you wanted to take out Autovocab, you would comment out or remove the lines 'elif ov00 eq 3, sets va01 "Autovocab"', and then change the next line 'elif ov00 eq 4' to 'elif ov00 eq 3', the next 'elif ov00 eq 5' to 'elif ov00 eq 4', and so on. This is annoying, so if you want to add other agents to automatically inject, I recommend doing that first to minimize the amount of renumbering you have to do.

This shows the above example. Note the changed numbers; you have to do this for all of the following 'elif ov00 eq ___' lines.
Two more notes on removing agents from the file: first, New Gadget Dropper has three lines you need to comment out or remove, because it actually has to be removed before it is injected. Make sure you get all three lines if you don't want it. Second, if you want to remove Wetness, please make sure that the lines 'doif gmap 1538 3272 eq -1, tick 0, endi' are not removed. If you remove New Gadget Dropper, make sure that the line 'tick 0' is not removed.

This shows what it would look like if you removed only Wetness and New Gadget Dropper.
There are two ways to add more agents to the list. First, you can replace one of the ones that's already there, if you don't want to inject that agent automatically. To do this, just find the name of that agent, then replace it with the name of the one you want to inject. The name must be exactly the same as it appears in the agent injector! For example, if you wanted to inject an agent called 'Foo' (its exact name in the agent injector), and didn't want the HLM Patch, you would change the line 'sets va01 "HLM Patch"' to 'sets va01 "Foo"'.

Again, very simple, but this shows the above example.
The second way is to add more lines, if you need to add more agents than you can by the first method. If it shows up in your DS agent injector, put them before the line that says 'do we have c3 in this world as well?'. If it is C3 only, add it after the line that says 'if you might ever make an undocked world'. The lines you will want to add are:
elif ov00 eq x
sets va01 "___"
Where x one more than the number in the previous 'elif ov00 eq _' line, and the text between the quotes in 'sets va01 "___" is the name of the agent exactly as it appears in the agent injector. You will also have to adjust all of the 'elif ov00 eq _' lines after your new addition to add one to the number for each new agent you add to the file.

This shows adding a new DS agent and a C3 only agent.
You can add as many extra agents as you like.
Before you try out your new file, please check that in all the lines of 'elif ov00 eq x', there are no numbers skipped (going from 'elif ov00 eq 4' to 'elif ov00 eq 6', for example) and there are no numbers that are listed twice.
If you get errors, first check the numbers to make sure that they are in order and that no number is skipped or appears twice. Second, if you changed out any of the agents or added new ones, make sure that the names are exactly as shown in the agent injector (the DS one for DS or C3/DS agents; the C3 one for C3 only agents). Third, make sure that you didn't accidentally add a C3 only agent before the 'EVERYTHING AFTER THIS POINT is a C3 agent;' line.
Good luck! I hope you find these files useful and are able to modify them to suit your purposes.
I would be very surprised if you have the exact same preferences for everything that I do, and there is probably at least one thing included in this by default that you don't like. Maybe you want your engineering icon after all the terrarium icons. Maybe you use a different autonamer. Maybe you have another twenty agents that you want to inject into almost every world that you make. Here's how to make that happen. Open up the .cos file you want to edit - I recommend CAOS Tool, or at least Notepad++, but a normal simple text editor (Notepad, gedit, etc) will work as well.
Making changes is not hard, even if you don't know any CAOS! However, because these files have permanent effects on new worlds, please test your changes on a temporary new world. I highly recommend making both an undocked and a docked test just to make sure that no errors pop up and nothing happens that you don't want to happen.
For the Anodyne part one file
If you don't want something to be removed, look for the line that says 'kill off ____' where ____ is the thing you want to keep. Either comment out the three lines following it (the ones that say enum ___, kill targ, next) by putting a * in front of them, or delete them.
(These demonstration images show commenting out because it is less destructive, but the effect is the same either way.)

This example shows how to keep the file from deleting the knowledge stones from your worlds.
If you want to have something else automatically removed, then add three lines in the section full of 'kill off ___' lines. If the agent is present in DS, do this before the line that says 'doif gmap 1538 3272 ne -1'. If the agent is present only in C3, it is best to put it AFTER the line that says 'doif gmap 1538 3272 ne -1'. The three lines you want to add are:
enum x y z
kill targ
next
Here x y z is the classifier number of the object you want to kill. If you don't know it, open up a world, hit ctrl-shift-t, and hover the hand over the object. Three numbers will come up on your screen. Record those three numbers and plug them into the 'x y z' exactly as they appeared in the game.

In this example, I added the classifier of the DS elevator buttons (maybe if you wanted to raze everything and use Elevines instead?).
If you don't want to turn off the Empathetic Vendor's hearing ability, either delete or comment out these lines by putting a * in front of them:
enum 2 23 3
setv ov00 0
part 1
pose 0
next

If you want to have the hand be called something other than "hand", change the line that says 'hand "hand"', to replace the "hand" with whatever you want the hand to be called. (Don't forget the quotes.)

You probably didn't need this image, but it's here for the sake of completeness.
If you want your room icons to be in a different order, go down to the part that says 'move camera to hallway' and then has a bunch of lines like this: cmra 6143 8998 0. The 'cmra 6143 8998 0' part is telling the game where to point the camera, so to change the order of your icons, you just have to change the order of those lines. I recommend changing the comments as well (the lines starting with **) to describe the new order, to keep from getting yourself confused. For example, if you wanted to have the Workshop icon be second, not the hallway icon, you would find the cmra line for the Workshop (cmra 4611 9039 0) and put it where the cmra line for the hallway is (cmra 2469 9046 0). Then you would take the cmra line for the hallway, and put it where the cmra line for the Workshop used to be. It is possible to change things around so that C3 icons can come before DS icons, as well.

This shows the above example.
For the Anodyne part two file
This file is actually easier to change than part one, woo! It also has the potential to cause errors. Be careful when modifying it!
Keep in mind that agents do not need to be in alphabetical order; I just did that to make things easier for me.
If you don't want to automatically add one of the agents in the file to your worlds (or you don't have it, etc), all you have to do is either comment out (add * before it) or take out the line that says 'sets va01 ___' (where ___ is the name of the agent), and the same to the 'elif ov00 eq ___' line just before it. You can also remove the comment (the line starting with **) if you want. Then, you must change all the following 'elif ov00 eq ___' lines following it to subtract one from whatever the 'eq ___' number is for every agent before that line that you removed. For example, if you wanted to take out Autovocab, you would comment out or remove the lines 'elif ov00 eq 3, sets va01 "Autovocab"', and then change the next line 'elif ov00 eq 4' to 'elif ov00 eq 3', the next 'elif ov00 eq 5' to 'elif ov00 eq 4', and so on. This is annoying, so if you want to add other agents to automatically inject, I recommend doing that first to minimize the amount of renumbering you have to do.

This shows the above example. Note the changed numbers; you have to do this for all of the following 'elif ov00 eq ___' lines.
Two more notes on removing agents from the file: first, New Gadget Dropper has three lines you need to comment out or remove, because it actually has to be removed before it is injected. Make sure you get all three lines if you don't want it. Second, if you want to remove Wetness, please make sure that the lines 'doif gmap 1538 3272 eq -1, tick 0, endi' are not removed. If you remove New Gadget Dropper, make sure that the line 'tick 0' is not removed.

This shows what it would look like if you removed only Wetness and New Gadget Dropper.
There are two ways to add more agents to the list. First, you can replace one of the ones that's already there, if you don't want to inject that agent automatically. To do this, just find the name of that agent, then replace it with the name of the one you want to inject. The name must be exactly the same as it appears in the agent injector! For example, if you wanted to inject an agent called 'Foo' (its exact name in the agent injector), and didn't want the HLM Patch, you would change the line 'sets va01 "HLM Patch"' to 'sets va01 "Foo"'.

Again, very simple, but this shows the above example.
The second way is to add more lines, if you need to add more agents than you can by the first method. If it shows up in your DS agent injector, put them before the line that says 'do we have c3 in this world as well?'. If it is C3 only, add it after the line that says 'if you might ever make an undocked world'. The lines you will want to add are:
elif ov00 eq x
sets va01 "___"
Where x one more than the number in the previous 'elif ov00 eq _' line, and the text between the quotes in 'sets va01 "___" is the name of the agent exactly as it appears in the agent injector. You will also have to adjust all of the 'elif ov00 eq _' lines after your new addition to add one to the number for each new agent you add to the file.

This shows adding a new DS agent and a C3 only agent.
You can add as many extra agents as you like.
Before you try out your new file, please check that in all the lines of 'elif ov00 eq x', there are no numbers skipped (going from 'elif ov00 eq 4' to 'elif ov00 eq 6', for example) and there are no numbers that are listed twice.
If you get errors, first check the numbers to make sure that they are in order and that no number is skipped or appears twice. Second, if you changed out any of the agents or added new ones, make sure that the names are exactly as shown in the agent injector (the DS one for DS or C3/DS agents; the C3 one for C3 only agents). Third, make sure that you didn't accidentally add a C3 only agent before the 'EVERYTHING AFTER THIS POINT is a C3 agent;' line.
Good luck! I hope you find these files useful and are able to modify them to suit your purposes.