Handle multi session better

[Soph]

Before:
When two sessions had interleaved checkpoints and the user committed, the second session's data would overwrite the first session's data on entire/sessions:

ab/c123def456/
├── metadata.json      # Only session B's metadata
├── full.jsonl         # Only session B's transcript
└── prompt.txt         # Only session B's prompts

After:
Both sessions are preserved with archiving:

ab/c123def456/
├── metadata.json      # session_count: 2, session_ids: [A, B], merged files_touched
├── full.jsonl         # Session B (most recent)
├── prompt.txt         # Session B
└── 1/                 # Session A (archived)
    ├── metadata.json
    ├── full.jsonl
    └── prompt.txt

---

Concurrent Session Warning Message

Before:

Another session is active with uncommitted changes. You can continue here, but
checkpoints from both sessions will be interleaved.

To resume the other session instead, close here and run: claude -r abc123

After:

Another session is active: "How about this logic: - if there is no folder..."

You can continue here, but checkpoints from both sessions will be interleaved.

To resume the other session instead, exit Claude and run: claude -r abc123

Press the up arrow key to get your prompt back.

And when resuming/rewinding:

  ---
  Scenario 1: Single session with local log newer
  $ entire resume feature/add-auth

  Switched to branch 'feature/add-auth'

  Warning: Local session log(s) have newer entries than the checkpoint:
    "Add JWT authentication to the API"
      Local last entry:      2026-01-14 15:32:18
      Checkpoint last entry: 2026-01-14 14:45:03

  Overwriting will lose the newer local entries.

    Overwrite local session logs with checkpoint versions? [y/N] y

  Session restored to: /Users/dev/.claude/projects/.../abc123.jsonl
  Session: 2026-01-14-abc123-uuid

  To continue this session, run:
    claude --resume abc123

  ---
  Scenario 2: Multi-session checkpoint with mixed statuses
  $ entire resume feature/refactor-db

  Switched to branch 'feature/refactor-db'

  Warning: Local session log(s) have newer entries than the checkpoint:
    "Refactor database connection pooling"
      Local last entry:      2026-01-14 16:20:45
      Checkpoint last entry: 2026-01-14 15:10:22

  These other session(s) will also be restored:
    "Add migration for users table" (new)
    "Fix failing tests in db_test.go" (checkpoint is newer)

  Overwriting will lose the newer local entries.

    Overwrite local session logs with checkpoint versions? [y/N] y

  Restored 3 sessions. To continue, run:
    claude --resume abc123  # Add migration for users table
    claude --resume def456  # Fix failing tests in db_test.go
    claude --resume ghi789  # Refactor database connection pooling (most recent)

  ---
  Scenario 3: No conflicts (proceeds without prompt)
  $ entire resume feature/new-feature

  Switched to branch 'feature/new-feature'
  Writing transcript to: /Users/dev/.claude/projects/.../xyz789.jsonl
  Session: 2026-01-14-xyz789-uuid

  To continue this session, run:
    claude --resume xyz789

[Soph]

Testing, entire/5325d1c was the branch based of the head commit in main. I used two agent sessions to do things and didn't commit in between. State after the second session see below:

test1234 on  entire/5325d1c [$] via 💎 v3.4.7
❯ find .entire
.entire
.entire/settings.json
.entire/logs
.entire/logs/2026-01-13-d488d465-0877-473a-8dc1-8a3e0c9c6f91.log
.entire/logs/2026-01-13-7bf322a0-638e-4284-80a5-f99654f343e2.log
.entire/.gitignore
.entire/metadata
.entire/metadata/2026-01-13-d488d465-0877-473a-8dc1-8a3e0c9c6f91
.entire/metadata/2026-01-13-d488d465-0877-473a-8dc1-8a3e0c9c6f91/full.jsonl
.entire/metadata/2026-01-13-d488d465-0877-473a-8dc1-8a3e0c9c6f91/context.md
.entire/metadata/2026-01-13-d488d465-0877-473a-8dc1-8a3e0c9c6f91/prompt.txt
.entire/metadata/2026-01-13-d488d465-0877-473a-8dc1-8a3e0c9c6f91/summary.txt
.entire/metadata/2026-01-13-7bf322a0-638e-4284-80a5-f99654f343e2
.entire/metadata/2026-01-13-7bf322a0-638e-4284-80a5-f99654f343e2/full.jsonl
.entire/metadata/2026-01-13-7bf322a0-638e-4284-80a5-f99654f343e2/context.md
.entire/metadata/2026-01-13-7bf322a0-638e-4284-80a5-f99654f343e2/prompt.txt
.entire/metadata/2026-01-13-7bf322a0-638e-4284-80a5-f99654f343e2/summary.txt
.entire/current_session

Then I did a commit in main branch, and looked at entire/sessions

test1234 on  entire/5325d1c [$] via 💎 v3.4.7
❯ git checkout entire/sessions
Switched to branch 'entire/sessions'

test1234 on  entire/sessions [$?]
❯ ls
e3

test1234 on  entire/sessions [$?]
❯ find e3
e3
e3/402324506f
e3/402324506f/full.jsonl
e3/402324506f/context.md
e3/402324506f/content_hash.txt
e3/402324506f/metadata.json
e3/402324506f/prompt.txt
e3/402324506f/1
e3/402324506f/1/full.jsonl
e3/402324506f/1/context.md
e3/402324506f/1/content_hash.txt
e3/402324506f/1/metadata.json
e3/402324506f/1/prompt.txt

test1234 on  entire/sessions [$?]
❯ cat e3/402324506f/metadata.json
{
  "checkpoint_id": "e3402324506f",
  "session_id": "2026-01-13-d488d465-0877-473a-8dc1-8a3e0c9c6f91",
  "strategy": "manual-commit",
  "created_at": "2026-01-13T11:37:42.258057+01:00",
  "checkpoints_count": 2,
  "files_touched": [
    "random_number.rb"
  ],
  "session_count": 2,
  "session_ids": [
    "2026-01-13-7bf322a0-638e-4284-80a5-f99654f343e2",
    "2026-01-13-d488d465-0877-473a-8dc1-8a3e0c9c6f91"
  ]
}%
test1234 on  entire/sessions [$?]
❯ cat e3/402324506f/1/metadata.json
{
  "checkpoint_id": "e3402324506f",
  "session_id": "2026-01-13-7bf322a0-638e-4284-80a5-f99654f343e2",
  "strategy": "manual-commit",
  "created_at": "2026-01-13T11:37:42.255509+01:00",
  "checkpoints_count": 1,
  "files_touched": [
    "random_number.rb"
  ],
  "session_count": 1,
  "session_ids": [
    "2026-01-13-7bf322a0-638e-4284-80a5-f99654f343e2"
  ]
}%

[Soph]

  Restored 2 sessions. Resume with:
    claude --continue uuid1  # Add password hashing...
    claude --continue uuid2  # Fix login validation... (most recent)

  For single-session checkpoints:
  claude --continue uuid1  # Add user authentication...````