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I've setup the folder structure for a new project following the pattern identified in sfdx-isv/sfdx-falcon-template. Also see this question Two SFDX project folder structure questions for some background.

When I add e.g. a new SObject in the scratch org and use:

sfdx force:source:pull

the new components are put in a fixed folder "main/default" - there is no option to nominate the correct folder. So the folder structure is compromised.

The change I am making in the scratch org is adding a new SObject and multiple fields: no sfdx commands at present to make that easy from the command line.

(When components are already present locally in folders other than "main/default" the pull does place the changes correctly.)

Is there a work-around here apart from just sticking to using "main/default" for everything or creating everything locally so the component can be setup in the right folder?

PS

Tried the manual workaround of pulling then moving the files locally but so far no joy: the move is seen as a delete that is bad news when you next push.

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Unfortunately, the CLI will always pull "Remote Add" metadata (ie. metadata not previously seen in any local SFDX Package Directory) into main/default/<metadata-type> inside of the default Package Directory specified in your project's sfdx-project.json file.

From the CLI's point of view, this behavior is by design. You need to have a place where previously unseen metadata can go, and <default-package-dir>/main/default provides that.

The part that needs fixing is the fact that the CLI is treating your subsequent reorganization (move) of your SFDX source files as a series of "Local Deletes" and "Local Adds" instead of just a simple "Local Moves".

Safe Harbor: The SFDX team is aware of this bug and is working on a fix. There is no ETA for when such a fix will be delivered. I'll update this answer once an ETA is available.

In the meantime, there are two ways you could work around this.

Workaround 1: Create a "local starter", push to scratch org, then customize in Setup UI

Technically, you can create your own metadata files locally and then do an initial push to your scratch org, even for those types that are more complex in SFDX, like customObjects.

Take a look at how an existing metadata type (object, permset, profile, etc.) is stored as SFDX source, copy that, then customize it as necessary for your new metadata component.

This isn't an elegant solution, but it does have the benefit of getting you comfortable with editing metadata files. For anyone who hasn't done this, it can be intimidating at first but you end up feeling like Neo seeing the Matrix once you've done it a few times. ;-)

Workaround 2: Build in Setup UI, reorganize locally in bulk, then rebuild your scratch org

You mentioned that you're aware of the SFDX-Falcon template. One of the things I like about SFDX-Falcon is the set of shell scripts provided in the dev-tools directory. They give a head start to anyone who wants to automate Salesforce CLI actions, and the one I use the most is rebuild-scratch-org.

If you know you're going to add a couple of custom objects and fields to your project, go ahead and build them in the Setup UI, pulling as you go without worrying about where the metadata is getting stored locally.

Once you're done with all the changes, open up a GUI file explorer and drag things out of <default-package-dir>/main/default and drop them wherever you want (as long as your destination is inside of an SFDX package directory).

Execute your rebuild-scratch-orgs shell script (which you've hopefully customized so that it does everything you need for a full scratch org build), and you'll be good to go. The CLI will know where everything is supposed to be from that point forward.

Closing Point: Is organizing my source worth all the trouble?

I definitely understand the frustration at not being able to fine-tune where new "Remote Add" metadata is saved by default. I still think it's worth the effort to come up with some logical structure that goes beyond the basic force-app/main/default that we get by default.

Your solution might not look exactly like SFDX-Falcon, but it's a good idea to do something, especially for projects based on large enterprise implementations and AppExchange packages.

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    Thanks for the detailed answer. I'll use the workarounds for now, but if the plugin fix doesn't happen on 2/10/18 its back to "main/default" for us... – Keith C Feb 3 '18 at 11:19
  • @KeithC - I just realized that my original answer was unclear. The plugin fix that's coming is supposed to make it possible to move metadata locally without causing the remote deletes. The way my answer originally reads it sounds like you'll be able to specify where new (unseen) metadata goes to by default. That won't be the case. I think there is good reason for this, by the way. I'll update my answer to address this. – Vivek M. Chawla Feb 3 '18 at 15:47
  • On the pull going to "main/default", having that as a default is fine. But if I know where I want the pull to go to (and can preview the pull using the status command) the option of nominating the location would make this a one step process rather than a two step process (of pull and then move). – Keith C Feb 4 '18 at 10:13
  • @KeithC - I agree with you. You make a good point about using force:source:status as a preview mechanism, too. I think the trick for the product team was trying to find a balance between flexibility and simplicity in terms of how the CLI exposes configurability that’s this granular. Even one step forward could be helpful, though. So, even if all we could do was say that all objects went HERE and all classes went THERE (and so on) it would eliminate at least some of the two-step process. Thank you for starting the discussion! – Vivek M. Chawla Feb 4 '18 at 13:45
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    Another possibility is to remove the sourcePathInfos.json from the .sfdx/org/{scratchOrgUserName}/ folder. This has the effect of remove the history from the local side. If you run another push SFDX will not see the "Delete" but rather match the current version in the new location with the version in the Scratch. A real wish item would be ability to push/pull only specific items at a time when needed. – John Head Feb 8 '18 at 15:31

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