`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.