`run` and `diff` use different directories

[Fryuni]

agentfs run uses sessions on ~/.agentfs/run/<id>/delta.db while agentfs diff looks for sessions on .agentfs/<id>.db (relative to current directory).

This makes the command suggested at the end of agentfs run fail.

Minimal reproduction transcript:

[lotus@lotus-notebook:/tmp/tmp.BvYnMXM3yR]$ agentfs -V
agentfs 0.6.2

[lotus@lotus-notebook:/tmp/tmp.BvYnMXM3yR]$ agentfs run bash
Welcome to AgentFS!

The following directories are writable:

  - /tmp/tmp.BvYnMXM3yR (copy-on-write)
  - /home/lotus/{.cache, .claude, .codex, .gemini, .local, .npm}

🔒 Everything else is read-only.

To join this session from another terminal:

  agentfs run --session 6754c191-24c4-4d8e-aac2-f49a469036bc <command>


[lotus@lotus-notebook:/tmp/tmp.BvYnMXM3yR]$ touch foo.txt

[lotus@lotus-notebook:/tmp/tmp.BvYnMXM3yR]$
exit

Session: 6754c191-24c4-4d8e-aac2-f49a469036bc

To resume this session:
  agentfs run --session 6754c191-24c4-4d8e-aac2-f49a469036bc

To see what changed:
  agentfs diff 6754c191-24c4-4d8e-aac2-f49a469036bc

[lotus@lotus-notebook:/tmp/tmp.BvYnMXM3yR]$ agentfs diff 6754c191-24c4-4d8e-aac2-f49a469036bc
Error: agent '6754c191-24c4-4d8e-aac2-f49a469036bc' not found at '.agentfs/6754c191-24c4-4d8e-aac2-f49a469036bc.db'

[lotus@lotus-notebook:/tmp/tmp.BvYnMXM3yR]$ ls -la ~/.agentfs
total 20
drwxr-xr-x   3 lotus users  4096 Feb 28 12:44 .
drwx------ 123 lotus users 12288 Feb 28 12:44 ..
drwxr-xr-x   4 lotus users  4096 Feb 28 12:52 run

[lotus@lotus-notebook:/tmp/tmp.BvYnMXM3yR]$ ls -la ~/.agentfs/run
total 16
drwxr-xr-x 4 lotus users 4096 Feb 28 12:52 .
drwxr-xr-x 3 lotus users 4096 Feb 28 12:44 ..
drwxr-xr-x 2 lotus users 4096 Feb 28 12:53 6754c191-24c4-4d8e-aac2-f49a469036bc

[lotus@lotus-notebook:/tmp/tmp.BvYnMXM3yR]$ ls -la ~/.agentfs/run/6754c191-24c4-4d8e-aac2-f49a469036bc/
total 228
drwxr-xr-x 2 lotus users   4096 Feb 28 12:53 .
drwxr-xr-x 5 lotus users   4096 Feb 28 12:59 ..
-rw-r--r-- 1 lotus users     19 Feb 28 12:52 base_path
-rw-r--r-- 1 lotus users   4096 Feb 28 12:52 delta.db
-rw-r--r-- 1 lotus users 214272 Feb 28 12:53 delta.db-wal

[lotus@lotus-notebook:/tmp/tmp.BvYnMXM3yR]$ cp ~/.agentfs/run/6754c191-24c4-4d8e-aac2-f49a469036bc/delta.db .agentfs/6754c191-24c4-4d8e-aac2-f49a469036bc.db

[lotus@lotus-notebook:/tmp/tmp.BvYnMXM3yR]$ agentfs diff 6754c191-24c4-4d8e-aac2-f49a469036bc
Using agent: 6754c191-24c4-4d8e-aac2-f49a469036bc
No diff (non-overlay filesystem)

When I copied the file it at least recognized it, but then it shows no diff, so there is another problem there. If I join the session again the changes are there.

[aaronS7]

I am also getting this issue as well. I just followed the quickstart and discovered this. Happy to help provide more details if needed on this!

[aaronS7]

Was able to get this fixed locally. I'll be honest, what I "did" was completely AI generated, but seems to work and test cases pass (along with a few other ones to catch it in the future). I'll try and create a PR for it. I'll also add the git diff for it in the meantime in case someone wants to fork there own until this is merged in.

Happy to make any changes to ensure it can keep the same standard as the rest of the code in the repo. Also if a more active contributor wants to just take the changes and make it better. Totally fine too

[aaronS7]

@Fryuni Here is the PR I created
#330

[aaronS7]

Saw that the build failed for windows, will work on addressing that later and testing on my windows machine