Hello everyone. In the interest of finally putting this particular topic to rest, in regards to the proper way to handle it - I've decided to create this thread and settle everything once and for all. There are lots of ins and outs to this, and there's been much misinformation spread about all of this over the years. Through much trial and error, I've figured out the best way of handling this process and having your content stay fully functional too. If you're interested in organizing your store content in this manner, then let's continue on.

"DECRAPIFYING"

A word I'm sure everyone in the TS3 community knows well by now. I'm going to put this to rest once and for all.

Decrapify, as most people know it, refers to running Sims3Packs through decrapify.exe, included as part of TS3 Recompressor (or S3RC, for short), which you can download here (Click the first link in the post to download, which is for Windows - which most people will be playing on.) While the two are basically the same thing, and Decrapify actually relies on S3RC to function - decrapify.exe does slightly more in the background than s3rc.exe does by itself. What most people use Decrapify for is being able to edit packages in S3PE, if they want to edit its contents. This is not possible by default, as S3PE will throw up an error if you try to open a converted package file from your store content - due to the encryption placed on it. Decrapify removes this encryption - which is, again, why most people use it. However, there are other side effects of this.

Decrapify itself renumbers the internal IDs and resources of Sims3Packs, essentially making the game treat it as a brand new or cloned item. It was originally created to fix certain Sims3Packs that wouldn't install after a certain update from EA. Though this was really only a problem for a short while, with very old Sims3Packs. It's more or less not needed nowadays.

When used on store content, it basically will break them. Due to the aforementioned renumbering, this will cause your content to not work properly - as the game expects the content to be structured a certain way internally. This, in turn, is why people need things like the Store Decrap Fixes to get them functional again. They are not needed otherwise. Decrap Fixes also inadvertently causes other issues if installed, such as causing buydebug to hang infinitely when going into it in-game. Also, if you decrapify your store content, then you'd also need to decrap any save files and other CC related to/using that content as well. So, bottom line - using decrapify.exe on your store content for any reason is really not recommended. It won't harm your game, but you'll have to do a bit more work to get it functional and keep it that way.

WHAT IF I WANT TO EDIT MY PACKAGES? WHAT DO I DO?

You're in luck, because there is another way. A much better method, that keeps your content working as designed by EA.

In the previous section I mentioned the tool known as S3RC. This tool's primary function is compressing CC content down to a smaller size, and is what most people use it for. A much less commonly known function of it, however, is the fact that it also removes the encryption of your store Sims3Packs and keeps them exactly the same as they were, unlike decrapify. No renumbering or other wonkiness.

All you need to do is drag the Sims3Pack over s3rc.exe, let go of it - and then a command prompt will open. You do not need to do anything else while it's open. Once it closes, that's it!

If you're 100% sure you'll never be doing anything with them in S3PE, you do not need to do this step.

HOW DO I CHANGE MY CONTENT INTO PACKAGES?

Easiest part of the whole process. All you need to do is download Delphy's Multi-Installer, extract it, tell it which folder to extract to and from (whichever folder your store Sims3Packs are located), and click "Install". It's recommended that you only extract one Sims3Pack at a time so you can keep track of what's what, but this isn't a requirement.

WHAT ABOUT THINGS LIKE STORE PATCHES/CCMERGED?

This is also very important, and something I definitely wanted to cover.

The ContentPatch (Store Patches) and ccmerged (required for your Premium Content to work properly) expects your store content to be installed a certain way. The standard way is installing through the Launcher, where it merges the content into .dbc and .ebc files (database files and encrpyted store files, respectively). The Launcher then places them inside of the DBCache folder in your Sims 3 Documents folder, along with a ccmerged.package that's updated anytime you install Premium Content items. When you install your store content as packages in your Mods folder, these will cease to operate properly by default. Because your content is installed in a way neither are expecting, they can no longer "see" that your content is installed. Fortunately, there is a workaround for this - one I've personally verified in-game.

To start, make absolutely sure that any of your store content that you're installing as package files goes specifically into your Mods/Packages folder (you have your Mods folder set up already, right?) If not, check the guide here. You can place them into a subfolder here if you want, but it must go into your Packages folder at the very least.

Next, you need to take your ContentPatch.package (inside of ContentPatch folder in Documents/The Sims 3) and ccmerged.package (inside of DBCache folder), and place both of them in your Overrides folder in your Mods folder. If you downloaded the Mod Framework directly from MTS, you should already have an Overrides folder. If not, use one of the tutorials around online and make one inside of your own Mods folder.

Please note that for the ccmerged.package however - you could possibly not already have one, or one that is fully updated. Since they are only created when installing Premium Content items through the Launcher, it could very well be that you don't have one if installing your content this way. Fortunately, downloading a fully updated ccmerged works just as well as if the game had created one itself. Nona's ccmerged file is one that people are commonly referred to as hers is fully up-to-date, and she has it available for download here (Scroll down to where it says "Download ccmerged.zip" and click it. Once the archive is downloaded, unzip it using 7-Zip or a similar program.)

What this basically does is make both of these resources load after your store content, and since they're now installed inside of your Mods folder with your store content - they will work exactly as they should. You should have no issues with any of your content, and moodlets and interactions should work as designed. If you use KT's Store Fixes (NOT the Decrap Fixes), then this should be installed here as well. None of these files will conflict with each other, as they're all affecting different things.

Furthermore, if you install any mods from here on out that are adjusting store content in any way, they should also be installed to Overrides as well so they can load before it. Alternatively, if you'd like to keep your store content separate from your mods and other CC in your Mods folder, check out zoe22's post below for further instructions.

WHAT IF MY CONTENT CONTAINS A VENUE/WORLD?

Another important point. Installing these types of contents means that you'll need to do some trial and error to figure out what's what. What do I mean by that? Well, when you extract packages from your store Sims3Packs, they'll often be split into multiple package files (unless it's a singular item). The bad thing about this is that they're extracted and named exactly the way their internal IDs appear, which is always a long string of numbers and letters. Something like this:

0xab906fc9a560123fb69fa20bjc

Very nondescript and unhelpful for organizing, isn't it? From here, what I recommend is using CUSTARD (Make sure to download the most recent version on Page 8 of the Comments, to ensure you have the proper category headers for the resources). What you need to do is open your store Sims3Pack through CUSTARD, find the particular resource you need, make note of the resource name (should look something like the example above), and install it to the respective location manually, optionally renaming them for better organization.

For Venues - Goes into your Library folder inside of Documents/The Sims 3 (Categorized as Lots in CUSTARD)
For Worlds - Game Installation Folder (NOT My Documents) \ Electronic Arts \ The Sims 3 \ GameData \ Shared \ NonPackaged \ Worlds (In CUSTARD, will possibly be marked as "Sims 3 Store Package" along with all other content inside of the Sims3Pack. If so, should be the one with the largest file size.) Before installing to your Worlds folder, make sure to rename the extension of at the end of the file name from .package to .world so that it will load properly in-game.

CLOSING

I think that should just about cover it! If you're a long-time TS3 player or new, I hope you found this guide informative or helpful in some way. I'd like to thank simsample for encouraging me to put this thread up for the benefit of all TS3 players out there.

Just to add that there is a bug with the store decrap fixes that causes infinite loading when going into buydebug. So that's another reason not to use the decrap tool.

Also this doesn't really matter but I think that putting something Overrides actually means the resources are loaded AFTER what's in Packages, so it will override the same-named resources that are in Packages, and be the ones that are used by the game.

I actually store my store content in a new folder in Mods called Store, and edited the resource.cfg file to give it a lower priority, so first store stuff is loaded, then packages, then overrides. So I can put store content related mods in Packages rather than overrides, as well as just having a separation from store content to regular mods which I like.
If anyone wants to do this, just add:

to resource.cfg and it should work (at least it seems to for me :p)

I've been trying to learn how to do this whole process. I've been successful in what is taught in this thread and followed all the steps. But what happens is that once I'm in the game, and edit town, the lot descriptions show file path names instead of the original names and addresses exp.. DOT4_world/emptyhouse etc.. Am I missing something or doing something wrong?
UPDATE: Sorry I figured it out. thanks for this thread, It's been very helpful!

^^ Not sure if this is how you fixed it, but I found that for store worlds installed as the .world file in the game files folder, I needed to have the STBL resources in Mods in order to work

A bit of serendipity that this thread was active so recently when I'm digging it up to say something-
I've been experimenting with the best ways to convert my store content, so I can do away with the launcher entirely, and haven't actually been able to recreate what this post describes at all. Not on worlds, venues, or individual items all downloaded myself from my store account. The IDs are identical regardless of which one is used.

Edit, to provide more useful information:
Experiments on Monte Vista have had the following results:
Brand new download of the TS3 Recompressor tool + Monte Vista downloaded from the Sims 3 Store, deleting DCCache, InstalledWorlds, and WorldCache each time.
ContentPatch and ccmerged in Overrides.

• Decrapify + S3RC is the most consistent and functional to use on worlds, both for installing through the launcher or manually. All appears as intended, but the pizza oven is missing its props, requires DecrapFixes.
• Only S3RC + launcher = outright broken. .world installed, but nothing else is installed to DCCache. World has no description, objects are missing ingame.
• Only S3RC + manual install = world only appears in menu if installed to the base game install directory, but works as intended. STBL are missing. Pizza oven is functional without fix.

Experiments with CUSTARD:
My personal desire was to avoid the untidiness of installing to the Program Files directory and the requirement for the STBL to be extracted and installed.

• I used CUSTARD to create a world-only copy of the Decrapped + S3RCed world. This installs correctly through the launcher- goes into InstalledWorlds, and the correct links are made in DCCache that provide the STBL and make the world appear on the main menu.
• Manual installing the objects from the Only S3RC pack manually doesn't work, they don't appear ingame
• Manual installing the objects from the Decrap+S3RC works, but pizza oven props are gone again. IDs are identical between these and the former, I have no clue what it is checking for that is so specific.
• Putting just the props from the S3RC objects in my Overrides fixes it, and I'm happy with that
• Edit #2: World-only launcher install + replacing the .world with the S3RC copy allows those objects to work while keeping the menu and STBL fixes. Props working

ALL of the above methods do not renumber the resources like a clone.
Unless someone can confirm that something about my setup could be preventing these tools from doing something they usually do, I don't really know where these corrections came from. I believe renumbering can only come about from using the -f command through the console, which was the function that fixed the old sims3packs and is not one that applies by default. Perhaps one of the older versions that used to circulate on the forums when these broken packs existed did?
Decrapify is described as a pruning tool, while S3RC compresses. They both do independent useful things, neither of which break content if they're used properly.
It's really only things with props that don't seem to like being 'pruned'. I can find them by their IDs in all versions, so it's some other connection that gets squashed somewhere.

Yes by extracting the xml STBL file and placing it there is the way