Cline checkpoints taking too long to initialize or stuck at 0 tokens?
When Cline says checkpoints are taking longer than expected, the model provider may not be the problem. Check the Git-backed workspace and checkpoint layer first, then verify the working tree before retrying.
git status and git diff before sending another request.What the failure looks like.
Cline may report that checkpoints are taking longer than expected to initialize, time out during checkpoint initialization, or show 0 tokens or 0 context after a request stalls. These UI states do not prove that your project files or partial edits disappeared.
Why Cline checkpoint initialization stalls.
Cline checkpoints use a separate shadow Git repository. Cline documents that very large repositories can make checkpoint commits slow, while its issue tracker shows that slow Git hooks can also block task activity. Multi-root workspaces are a separate limitation: Cline disables checkpoints there because coordinating multiple Git histories is not supported.
Fix the checkpoint timeout without losing the task.
git status and inspect git diff. Record any partial edits, the failed attempt, and the last test that actually ran.Does disabling checkpoints delete files?
No. Cline checkpoints are snapshots stored in a shadow Git repository separate from your project history. Turning them off removes Cline's checkpoint rollback feature; it does not delete the files in your working tree. Your normal Git history remains the safer source of truth while diagnosing the timeout.
What the next AI should receive.
The diff and changed files are the evidence. Add the task goal, known constraints, last successful check, and the checkpoint failure so the next agent does not assume the empty context display means nothing changed.
Immediate recovery
Open one Git-backed folder, disable checkpoints if initialization remains blocked, and verify the working tree before retrying.
What survives
Git status, the diff, changed files, local notes, and test output remain available even when Cline's context panel is empty.
Trust boundary
A 0-token display is a UI state, not evidence about the repository. Treat the disk and test output as the facts to verify.
How ShardStitch helps.
ShardStitch scans local project state and builds a continuation packet for Cline or another supported AI tool. It separates verified disk facts from inferred session claims, preserving changed files, decisions, failed attempts, verification status, and the next safe action without asking the stalled session to summarize itself.
Source trail.
Cline's checkpoint documentation explains the shadow Git repository, the settings toggle, and the large-repository performance warning. Cline issue #4578 documents blocked task activity and the checkpoint/Git-hook interaction. Cline issue #1782 documents the separate 0-token/context stall.
FAQ.
How do I fix "checkpoints are taking longer than expected to initialize"?
Open Cline in a single Git-backed project. If initialization still stalls, disable Enable Checkpoints under Cline Settings > Feature Settings, then inspect the working tree before retrying.
Should I retry Cline immediately?
No. Verify the files and record the failure first. A second attempt should start from known state, not an unverified session claim.
What if the old session is already gone?
Recover the current goal, changed files, git state, decisions, failed approaches, verification status, and next action from the project and available local artifacts.
Can the work move to another AI tool?
Yes, when the project state is available locally. The continuation packet carries useful state into a fresh session or another supported tool.
Scope note: This page separates Cline checkpoint initialization failures from provider API failures. Behavior can vary by Cline version, operating system, repository size, workspace layout, and Git hooks.