CLI Performance Regression After Enabling Full Repository

[dhanushk-offl]

What happened?

After enabling the entire repository for the CLI/agents, the overall performance has become significantly slower.

Almost every action now takes much longer than before:

• Giving an agent a task can take 2–3 minutes before the task is completed.
• Agent operations that previously felt relatively quick now have noticeable delays.
• Even basic Git operations are affected. For example, running a local commit can take several minutes and may eventually hit the 120-second command timeout.
• The slowdown appears to happen broadly across the CLI rather than being limited to a specific task.

Expected Behavior

Enabling the entire repository should not cause normal CLI operations, agent tasks, or local Git commands to become significantly slower.

Git operations such as git add and git commit should complete within a reasonable amount of time unless the repository itself has an unusually expensive operation configured.

Actual Behavior

After enabling the entire repository:

• Agent tasks take around 2–3 minutes to execute.
• CLI actions generally feel significantly slower.
• Local Git commits can take several minutes.
• Commands may exceed the default 120-second timeout.

Impact

This makes the CLI difficult to use for normal development workflows because even small changes and simple tasks require waiting several minutes.

Possible Area to Investigate

It may be related to the CLI scanning, indexing, analyzing, or processing the entire repository on each action. It would be useful to check whether repository-wide context/indexing is being unnecessarily repeated for every command or agent operation.

Steps to reproduce

Steps to Reproduce

1. Open a repository in the CLI.

2. Enable the entire repository using:

   entire enable

3. Make a small change to any file in the codebase.

4. Stage the change:

   git add <changed-file>

5. Commit the change:

   git commit -m "test: verify commit performance"

6. Observe that the commit operation takes significantly longer than expected and may take several minutes or exceed the CLI's 120-second timeout.

7. Additionally, assign a normal task to an agent after enabling the entire repository and observe that task execution can take 2–3 minutes.

Entire CLI version

0.10.2

OS and architecture

OS/Arch: linux/amd64

Agent

Codex, OpenCode

Terminal

Fish

Logs / debug output

$ git add src/components/field/voice-element.tsx && git commit -m "Git Commit to the status"
(no output)

<shell_metadata>
shell tool terminated command after exceeding timeout 120000 ms. If this command is expected to take longer and is not waiting for interactive input, retry with a larger timeout value in milliseconds.
</shell_metadata>

Additional context

git version 2.54.0
shell:fish

[Soph]

Thanks for opening this, we are are having a related issue open #2091

We enabled flagging slow hooks in logfiles last week so it's part of 0.10.2 but I only merged #2092 today which will make aggregation easier by running entire doctor trace --summary --slow --last 500

If you want could you run entire doctor bundle and send the result to my firstname @entire.io ? Happy to take a look.

Also another thing worth trying is the nightly release since we merged #2002 tonight which should improve log writing performance. Especially with codex.

To install nightly you can use curl -fsSL https://entire.io/install.sh | bash -s -- --channel nightly