AugustaCalidia

Could you please provide a link to the "Vortex author's" remark? It would be strange for him to claim that Skyrim does not support hard links and then create a mod manager whose core deployment method for Bethesda (and many other) games is hard link deployment. Regardless, the files in my Skyrim game data folder are definitely hard links to and not "physical" copies of the mods in the Mod Staging Folder.
 
Seeing an icon in your game data folder is not a test for whether the file is a hard link or a "physical" copy. I see icons too, but I can independently verify that the files in question are hard links.

You'll get better results by posting your issue in a Skyrim SE support forum. This forum is the Vortex support forum.

View Gopher's Vortex tutorials. Start here:
 

 
You don't need standalone LOOT. LOOT is built into Vortex.

"My Time at Portia" appears not to be supported by Vortex. I can find no game extension for it. At present, Vortex support is available for only about 140 of the over 1000 games whose mods are hosted on Nexus Mods.

You need to take your issue to an MO2 support forum. This is the Vortex support forum.

Open a thread here: https://forums.nexusmods.com/index.php?/forum/117-feedback-suggestions-and-questions/.

You don't see the game in "Unmanaged" because currently there is no Vortex support for the game. Without a Vortex extension, the game will not be recognized.
 
Vortex is open source. Many of the new game extensions are being written by the game players themselves. Find a fellow gamer with the programming skills and ask him/her to develop an extension.
 
By the way, you don't need a mod manager to do the modding. You can do it the old fashioned way - manually.

This is an issue for a Fallout NV support forum. This is not a Vortex problem.

Vortex currently manages only about 130 of the over 1000 games whose mods are hosted on the Nexus Mods website. Your games, including "Alien: Isolation," may not yet be managed by Vortex. To see if a game is managed by Vortex, check the Extensions tab on the Vortex dashboard. Also, check here: https://www.nexusmods.com/site/mods/categories/4/?BH=2. If no game extension is listed, then the game is not supported.
 
Since Vortex is open source and works via extensions, you can write your own game extensions and submit them to the devs to be added to the extensions library. Here is a template with instructions: https://wiki.nexusmods.com/index.php/Creating_a_game_extension_for_Vortex.

What happens if you click on "Show Hidden Games?"

Reinstall Vortex over the old installation. That will not delete your mods, as they are not in the Vortex installation folder (unless you mistakenly put them there). I have reinstalled Vortex this way with every iteration of Vortex since its alpha days, and I have not lost a single mod.

@HadToRegister is correct - "The Witcher 3" is a weird one. For hardlink deployment to work, you need to have the game, the mod staging folder, and the game settings folder all on the same drive. The game settings folder is "The Witcher 3" located in your Windows Document folder from which it cannot be moved. Since Documents is installed to drive C:\ by default, then you need to install the game and the mod staging folder to that drive as well.
 
Here is a suggestion that may or may not work. Use at your own risk. Try relocating Documents to drive D:\, as @HadToRegister and @rmm200 suggested. WARNING: under no circumstances should you try to cut and paste the Documents library to drive D:/! Rather, use the special move function that Windows utilizes for Windows library folders, as @rmm200 has already suggested.

Yes. Upper right hand of Plugins Page UI.

Vortex ----> Settings ----> Interface ----> Dashlets ----> Starter. Disable Starter and re-enable. If that doesn't work, then disable Starter, exit Vortex, relaunch Vortex, and then enable Starter.

Read this recent thread: https://forums.nexusmods.com/index.php?/topic/9131113-random-microsoft-flight-simulator-file/&do=findComment&comment=85369153.

Open a thread on a Fallout 4 support forum. There you will find the help you need. This is the Vortex support forum.

As Gopher's video tutorial shows, you drag the script extender archive into the Drop File(s) box at the bottom of the Mods Page, not the Extensions Page. The script extender archive contains a mod, not a Vortex extension.

On the Vortex mods page double-click to open the mod details panel. The "mod type" box is at the bottom of the panel.

https://www.nexusmods.com/site/mods/103.

Read this: https://help.nexusmods.com/article/105-i-have-reached-a-daily-or-hourly-limit-api-requests-have-been-consumed-rate-limit-exceeded-what-does-this-mean.

Go to the Vortex plugins page and assign the plugin to a late loading LOOT group. Double clicking the .esp opens a right hand panel where you can make the group assignment. There's no need to make a bunch of rules.
 
Out of curiosity, what is your game, what is the mod, and does the plugin work where LOOT/Vortex placed it? I would certainly recommend following the advice of the mod author to load last. However, many mod authors offer that advice out of an abundance of caution. Very few plugins ever need to be absolutely last in a load order. Only if the plugin affected the performance of every other plugin in the load order would it have to be last.

It sounds as if you may be installing a Skyrim LE mod on Skyrim SE. Check to see whether or not you're using the Skyrim SE version of the mod. Skyrim LE mods are generally not compatible with Skyrim SE.

In Version 1.1.15 "Unmanaged" has replaced "Discovered." Apparently the instructions have not been updated. If you have a Vortex supported game on your computer, it will show up in color in the "Unmanaged" section.

This is the Vortex support forum. Your questions are best raised on the appropriate Skyrim and Enderal support forums. However, two comments here.
 
1. Skyrim and Steam Enderal are two separate games and two separate downloads. Mods you install for Enderal will not be installed for Skyrim.
2. To install Skyrim mods into Enderal, manually download the archive and then drop it into the drop box at the bottom of the Enderal mod page in Vortex.

Clicking on "Remove" brings up a menu with options to remove mods only or archives only or both. If you select mods only, that empties your Mod Staging Folder but leaves your archive downloads intact. Those archives will show up as "Uninstalled" on your Mods page.