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This is still an issue.

I'm working on a PR that might fix this as a side effect. We'll see... I'm currently stuck trying to get ruby installed on my MBP so I can test if I break the mobile app. I think based on what I'm seeing in your issue here and the unit test cases I wrote, it should be fine :)

Hopefully if that works out, I should hopefully have it out sometime soon (next few days?). That being said, I've only written unit tests. Now that I think about it, I should add E2E tests... I'll have to play with that.

I'm wrapping up what I think will be a draft PR. I just finished testing my changes on iOS (it took years off my life) and I have not written end-to-end tests (just unit), but I'll open the PR as WIP: and gauge if they should be written and good next steps.

My PR should solve these issues. I think there are a couple other issues that we might want to consider in the future regarding org-mode/roam aliases and Logseq, but for now given your reproduction steps it should be sufficient. The root of the problem is the incorrect parsing of file-paths due to buggy platform-specific path resolution for missing files which seems unnecessary in my testing. The non-compliant file url you are seeing ([[file:..//Users/user/logseq-home/pages/Alias.org][Alias]]) also occurs when linking to any non-existent page. It seems like Logseq handles creation of those pages files, but Org Roam will freak out (since that file path makes no sense anyways).

We can discuss later, but here are some questions I have for future development:

1. Should the ::alias <alias> shorthand expand to the Org #+ALIAS tag?
   • The "Aliases and external links" section only gives instructions for ::alias, which still gives you hints for using it when in Org. Mashing enter will not create is as a recognized Logseq alias however.
   • #+ALIAS does not have any hints that it is a reserved keyword like ::alias does.
2. Should the #+ALIAS: <alias> be placed in the standard Org :PROPERTIES: section?
3. Should there be functionality to provide better integration with Org-Roam?
   • Org-Roam uses the :ROAM_ALIASES: <alias> tag in the :PROPERTIES: section instead of :ALIAS:
   • #+ROAM_ALIASES: under the :PROPERTIES: does not appear to be recognized in Org Roam in my testing.
   • :ROAM_ALIASES: in :PROPERTIES: is not recognized by Logseq, but :ALIAS: in properties is.
   • Implementation of this compatibility would need to be discussed more broadly.
     • Recognizing :ROAM_ALIASES: in Logseq seems like it would probably be relatively easy (I haven't actually checked though...). We would maybe also want to have an option for the "alias syntax" so that creation of aliases can be Org-Roam compatible (although there is no way of creating aliases non-manually anyways, like a ::alias expansion).
     • It's possible that Org-Roam could also be enabled to recognize :ALIAS: through a third-party plugin of some kind. Perhaps there is already a built-in configuration for this, I'm not sure. It's honestly a bit strange to me that :ALIAS: isn't support already. I'm not sure if it's reserved for other purposes...

Hopefully I can post my draft PR tonight or tomorrow. I'm happy to see that my fix should solve your issues. I have to run to a social event, but hopefully you'll see my PR soon.

👋

EDIT: I just realized that you're the person who created the org-roam-logseq.el repo that I forked and linked about (which is based off another's gist). Funny....