Use the table of contents to navigate to whichever mission you're currently doing. The numbering order was determined by where all the maps were moved to in the new layout.

Yellow box -> chest or loot
-This icon covers all types of chests as well as the 'unidentified blueprint'. The icon's size is not indicative of what type of chest/loot is there.

Blue 'Diamond' -> info-fragment
-For revealing the contents of end-crusade loot chests. Omicron Arkh has a voice line that lets you know when one is nearby. (I realize this icon is pixellated in the mission maps)

Red Box -> cogitator for unlocking covert missions

Red Diamond -> covert mission (this is a crusade map icon)

Purple Oval -> teleporter
-Only teleporters that go to "off-map" rooms are marked.

Green Star -> relevant secondary objective
-Only secondary objectives that unlock something upon successful completion are marked.

Note about the mission maps:
I've rotated them to at least approximately match how the map is oriented at the start of the mission.

https://steamproxy.net/sharedfiles/filedetails/?id=2224879780
The numbers below have been converted to my numbering.

"Mastery Path"
3 - 4 - 7 - 2 - 13 -
12 - 17 - 20 - 18 - 5 -
6 - 9 - 10 - 21 - A -
14 - 15 - B - E - C -
16 - 19 - 11 - 1 - 8 -
D - Z

Completing this mission, as well as mission 15, unlocks Secret Mission B.

Unlocked via completion of Mission 13.

Completing this mission unlocks Mission 12.

Completing this mission, as well as mission 10, unlocks Secret Mission B.

Must successfully aid the Stormwatcher to unlock the cogitator which unlocks Covert Mission D.

Cogitator unlocks Covert Mission C.

Unlocked by completing missions 10 and 15. Completing this mission unlocks Covert Mission E.

Unlocked via the cogitator in Secret Mission A.

Unlocked via the cogitator in mission 18.

Unlocked via the completion of Secret Mission B.

Nothing here.

Let me know if I missed anything or if there are any typos/formatting issues.

Credits:
https://steamproxy.net/profiles/76561198007133336 for helping test unlock conditions for mission B
https://steamproxy.net/id/Winged_Human for notifying me of changes to a mission unlock condition
https://steamproxy.net/profiles/76561198092241169 for the 6/7/23 update

Patch notes:
4/01/20 ->
-linked the ecru guide, updated the "Note about the mission maps"
5/25/20 ->
-linked the amber guide
-updated the Crusade Map and Final Notes sections
-updated maps for missions 8 and C and Y
5/30/20 ->
-fixed unlock conditions for mission B
-remove an extraneous item from the map key
-added Credits section to Final Notes
6/26/20 ->
-linked the viridian and azure guides
-noted which links go to which guides for ease of reference
10/29/20 ->
-added notes under certain missions and updated the titles of certain missions to make unlock conditions easier to reference
-linked the Zircon guide
2/12/21 ->
-updated a mission unlock condition, added a credit
-linked the Violet guide, linked a fellow guide-writer's void crusade path recommendations
8/18/22 ->
-linked the Crimson guide
6/7/23 ->
-added a section for Grimstalker's recommended path
-changed the link to Grimstalker's stuff from the general link to the link for the specific crusade and moved it to the dedicated section from the basic guide info section