R1.a: real-app RPC and filesystem transcript; synthetic data only.
Before: 8ee7183e6c; after: 5ac4ccb47f. Viewport/theme: N/A.
Ordered stages: create project and active branched thread through RPC -> intact scan -> remove only managed fixture worktree -> fresh scan -> reload client -> scripted picker selection -> fresh after scan (server traced from startup) -> filesystem checks.
RPC excerpts omit unrelated machine inventory and model catalogs; fixture fields are preserved. No provider turn was sent.

BEFORE
{
  "projectId": "cdc37f52-b1f2-4199-acd1-7ce593748b68",
  "threadId": "3c74ef27-9649-4b81-b380-439069f4af02",
  "branch": "evidence-before-r3",
  "worktreePath": "/home/user/wt/pr-32471-cap2-before/.t3/worktrees/fixture-project/evidence-before-r3-81ea1418da4d9125",
  "projectRoot": "/tmp/lead-32471-r2/evidence-capture-2/run-20261110T170228356308Z/fixture-project",
  "archived": false
}
{
  "start": "2026-11-10T17:07:02.618Z",
  "end": "2026-11-10T17:07:03.165Z",
  "method": "server.refreshProviders",
  "request": {
    "instanceId": "claudeAgent",
    "cwd": "/home/user/wt/pr-32471-cap2-before/.t3/worktrees/fixture-project/evidence-before-r3-81ea1418da4d9125",
    "fresh": true,
    "workspaceSnapshotsOnDemand": true,
    "providerCatalogsOnDemand": true
  },
  "responseExcerpt": {
    "instanceId": "claudeAgent",
    "workspaceSnapshots": [
      {
        "cwd": "/home/user/wt/pr-32471-cap2-before/.t3/worktrees/fixture-project/evidence-before-r3-81ea1418da4d9125",
        "checkedAt": "2026-11-10T17:07:02.625Z",
        "slashCommands": [],
        "skills": []
      }
    ]
  }
}
Selection serialization: {"serialized": "$finalize", "menuOpen": false}

AFTER
{
  "projectId": "74b4d5e4-ac78-4552-a4e8-d4a49c07f127",
  "threadId": "a69121fa-795f-4dae-a699-0023c0d09d0c",
  "branch": "evidence-after-r3",
  "worktreePath": "/home/user/wt/pr-32471-cap2-after/.t3/worktrees/fixture-project/evidence-after-r3-c377d729f7698838",
  "projectRoot": "/tmp/lead-32471-r2/evidence-capture-2/run-20261110T170228356308Z/fixture-project",
  "archived": false
}
{
  "start": "2026-11-10T17:07:46.480Z",
  "end": "2026-11-10T17:07:50.198Z",
  "method": "server.refreshProviders",
  "request": {
    "instanceId": "claudeAgent",
    "cwd": "/home/user/wt/pr-32471-cap2-after/.t3/worktrees/fixture-project/evidence-after-r3-c377d729f7698838",
    "fresh": true,
    "workspaceSnapshotsOnDemand": true,
    "providerCatalogsOnDemand": true
  },
  "responseExcerpt": {
    "instanceId": "claudeAgent",
    "workspaceSnapshots": [
      {
        "cwd": "/home/user/wt/pr-32471-cap2-after/.t3/worktrees/fixture-project/evidence-after-r3-c377d729f7698838",
        "checkedAt": "2026-11-10T17:07:46.499Z",
        "slashCommands": [
          {
            "name": "finalize",
            "description": "Finalize the fixture change (project)"
          },
          {
            "name": "finalize-command",
            "description": "Finalize the synthetic command fixture (project)"
          }
        ],
        "skills": [
          {
            "name": "finalize",
            "description": "Finalize the fixture change",
            "path": "/tmp/lead-32471-r2/evidence-capture-2/run-20261110T170228356308Z/fixture-project/.claude/skills/finalize/SKILL.md",
            "scope": "project",
            "enabled": true
          }
        ]
      }
    ]
  }
}
Selection serialization: {"serialized": "$finalize ", "menuOpen": false}
Fresh after selection (server traced from startup):
{
  "start": "2026-11-10T17:10:19.978Z",
  "end": "2026-11-10T17:10:22.276Z",
  "method": "server.refreshProviders",
  "request": {
    "instanceId": "claudeAgent",
    "cwd": "/home/user/wt/pr-32471-cap2-after/.t3/worktrees/fixture-project/evidence-after-r3-c377d729f7698838",
    "fresh": true,
    "workspaceSnapshotsOnDemand": true,
    "providerCatalogsOnDemand": true
  },
  "responseExcerpt": {
    "instanceId": "claudeAgent",
    "workspaceSnapshots": [
      {
        "cwd": "/home/user/wt/pr-32471-cap2-after/.t3/worktrees/fixture-project/evidence-after-r3-c377d729f7698838",
        "checkedAt": "2026-11-10T17:10:20.015Z",
        "slashCommands": [
          {
            "name": "finalize",
            "description": "Finalize the fixture change (project)"
          },
          {
            "name": "finalize-command",
            "description": "Finalize the synthetic command fixture (project)"
          }
        ],
        "skills": [
          {
            "name": "finalize",
            "description": "Finalize the fixture change",
            "path": "/tmp/lead-32471-r2/evidence-capture-2/run-20261110T170228356308Z/fixture-project/.claude/skills/finalize/SKILL.md",
            "scope": "project",
            "enabled": true
          }
        ]
      }
    ]
  }
}

Verbatim synthetic-path excerpts from the after server started under strace -f -e trace=%file -s 300.
The full private syscall log is intentionally not uploaded.

Missing requested directory:
3105588 access("/home/user/wt/pr-32471-cap2-after/.t3/worktrees/fixture-project/evidence-after-r3-c377d729f7698838", F_OK) = -1 ENOENT (No such file or directory)
3105586 statx(AT_FDCWD, "/home/user/wt/pr-32471-cap2-after/.t3/worktrees/fixture-project/evidence-after-r3-c377d729f7698838", AT_STATX_SYNC_AS_STAT|AT_SYMLINK_NOFOLLOW, STATX_ALL, 0x7d5b617f6a50) = -1 ENOENT (No such file or directory)
3105587 access("/home/user/wt/pr-32471-cap2-after/.t3/worktrees/fixture-project/evidence-after-r3-c377d729f7698838/.git", F_OK) = -1 ENOENT (No such file or directory)
3105585 access("/home/user/wt/pr-32471-cap2-after/.t3/worktrees/fixture-project/evidence-after-r3-c377d729f7698838/.git", F_OK) = -1 ENOENT (No such file or directory)

Project-root file: .claude/skills/finalize/SKILL.md
3117795 openat(AT_FDCWD, "/tmp/lead-32471-r2/evidence-capture-2/run-20261110T170228356308Z/fixture-project/.claude/skills/finalize/SKILL.md", O_RDONLY|O_NOCTTY|O_LARGEFILE|O_CLOEXEC <unfinished ...>
3117795 <... openat resumed>)           = 17
3117795 openat(AT_FDCWD, "/tmp/lead-32471-r2/evidence-capture-2/run-20261110T170228356308Z/fixture-project/.claude/skills/finalize/SKILL.md", O_RDONLY|O_LARGEFILE|O_CLOEXEC|O_PATH <unfinished ...>
3117795 <... openat resumed>)           = 22
3117794 openat(AT_FDCWD, "/tmp/lead-32471-r2/evidence-capture-2/run-20261110T170228356308Z/fixture-project/.claude/skills/finalize/SKILL.md", O_RDONLY|O_NOCTTY|O_LARGEFILE|O_CLOEXEC <unfinished ...>
3117794 <... openat resumed>)           = 14
3117840 openat(AT_FDCWD, "/tmp/lead-32471-r2/evidence-capture-2/run-20261110T170228356308Z/fixture-project/.claude/skills/finalize/SKILL.md", O_RDONLY|O_LARGEFILE|O_CLOEXEC|O_PATH <unfinished ...>
3117840 <... openat resumed>)           = 23

Project-root file: .claude/commands/finalize-command.md
3117795 openat(AT_FDCWD, "/tmp/lead-32471-r2/evidence-capture-2/run-20261110T170228356308Z/fixture-project/.claude/commands/finalize-command.md", O_RDONLY|O_NOCTTY|O_LARGEFILE|O_CLOEXEC <unfinished ...>
3117795 <... openat resumed>)           = 16
3117829 openat(AT_FDCWD, "/tmp/lead-32471-r2/evidence-capture-2/run-20261110T170228356308Z/fixture-project/.claude/commands/finalize-command.md", O_RDONLY|O_LARGEFILE|O_CLOEXEC|O_PATH) = 16
3117795 openat(AT_FDCWD, "/tmp/lead-32471-r2/evidence-capture-2/run-20261110T170228356308Z/fixture-project/.claude/commands/finalize-command.md", O_RDONLY|O_NOCTTY|O_LARGEFILE|O_CLOEXEC) = 12
3117840 openat(AT_FDCWD, "/tmp/lead-32471-r2/evidence-capture-2/run-20261110T170228356308Z/fixture-project/.claude/commands/finalize-command.md", O_RDONLY|O_LARGEFILE|O_CLOEXEC|O_PATH <unfinished ...>
3117840 <... openat resumed>)           = 22


Synthetic fixture filesystem state after scans and picker selection.
2026-11-10T17:11:55.444047+00:00

before 8ee7183e6c8a1c22a6698f4909ef7e2a423bec3a
$ ls -ld /home/user/wt/pr-32471-cap2-before/.t3/worktrees/fixture-project/evidence-before-r3-81ea1418da4d9125
ls: cannot access '/home/user/wt/pr-32471-cap2-before/.t3/worktrees/fixture-project/evidence-before-r3-81ea1418da4d9125': No such file or directory
exit=2
$ git -C /tmp/lead-32471-r2/evidence-capture-2/run-20261110T170228356308Z/fixture-project branch --list evidence-before-r3
  evidence-before-r3
exit=0
$ git -C /tmp/lead-32471-r2/evidence-capture-2/run-20261110T170228356308Z/fixture-project status --porcelain

exit=0

after 5ac4ccb47fd2888646f1776445d701c504b87e1f
$ ls -ld /home/user/wt/pr-32471-cap2-after/.t3/worktrees/fixture-project/evidence-after-r3-c377d729f7698838
ls: cannot access '/home/user/wt/pr-32471-cap2-after/.t3/worktrees/fixture-project/evidence-after-r3-c377d729f7698838': No such file or directory
exit=2
$ git -C /tmp/lead-32471-r2/evidence-capture-2/run-20261110T170228356308Z/fixture-project branch --list evidence-after-r3
  evidence-after-r3
exit=0
$ git -C /tmp/lead-32471-r2/evidence-capture-2/run-20261110T170228356308Z/fixture-project status --porcelain

exit=0

AI-assisted; verified with the tests and tools listed above.