Please add support for Claude-Code Native CLI Installation

[imdeveloper01]

TweakCC patches fail to apply to Claude's native installation (which is recommended by Anthropic over npm)

Error: Failed to extract claude.js from native installation
at ur (file:///mnt/c/[path]/node_modules/tweakcc/dist/config-ChxM7yMT.mjs:667:10780)
at async Gt (file:///mnt/c/[path]/node_modules/tweakcc/dist/index.mjs:26:133)
at async Command. (file:///mnt/c/[path]/node_modules/tweakcc/dist/index.mjs:24:1708)

Claude native uses the version name as the binary (i.e. claude/versions/2.1.8.5) over just 'claude'

[bl-ue]

Hi @nwtfdev! tweakcc does support patching native Claude Code installations, on macOS, Windows, and Linux. It looks like you're using CC 2.1.85 on Windows via WSL. Will you please run npx tweakcc@latest --apply --debug and attach the full output here?

[viceversaco]

looks like you have node and tweakcc installed in Windows but are trying to use a Windows installed node package with WSL. I'd suggest using node and tweakcc in WSL, not in Windows.

[imdeveloper01]

Hi @nwtfdev! tweakcc does support patching native Claude Code installations, on macOS, Windows, and Linux. It looks like you're using CC 2.1.85 on Windows via WSL. Will you please run npx tweakcc@latest --apply --debug and attach the full output here?

npx tweakcc@latest --apply --debug
Applying saved customizations to Claude Code...
Configuration saved at: /[USER_HOME]/.claude/tweakcc/config.json
Reading config at /[USER_HOME]/.claude/tweakcc/config.json
getClaudeFromPath: Found claude at /[USER_HOME]/.local/bin/claude
Checking claude on PATH: /[USER_HOME]/.local/bin/claude
resolvePathToInstallationType: /[USER_HOME]/.local/bin/claude -> /[USER_HOME]/.local/share/claude/versions/2.1.89
resolvePathToInstallationType: Detected mime type: application/x-executable
extractVersion: Got version 2.1.89 from filename
Using Claude Code from PATH: /[USER_HOME]/.local/share/claude/versions/2.1.89 (native-binary, v2.1.89)
Skipped 229 up-to-date file(s)

Created 8 new prompt file(s):
/[USER_HOME]/.claude/tweakcc/system-prompts/skill-computer-use-mcp.md
/[USER_HOME]/.claude/tweakcc/system-prompts/system-prompt-buddy-mode.md
/[USER_HOME]/.claude/tweakcc/system-prompts/system-prompt-mcp-tool-result-truncation.md
/[USER_HOME]/.claude/tweakcc/system-prompts/system-prompt-partial-compaction-instructions.md
/[USER_HOME]/.claude/tweakcc/system-prompts/system-prompt-powershell-5.1.md
/[USER_HOME]/.claude/tweakcc/system-prompts/system-prompt-remote-plan-mode-ultraplan.md
/[USER_HOME]/.claude/tweakcc/system-prompts/system-prompt-remote-planning-session.md
/[USER_HOME]/.claude/tweakcc/system-prompts/tool-description-config.md

Updated 18 system prompt file(s):
agent-prompt-general-purpose.md (2.1.84 → 2.1.86)
agent-prompt-security-monitor-for-autonomous-agent-actions-second-part.md (2.1.85 → 2.1.89)
agent-prompt-verification-specialist.md (2.1.72 → 2.1.89)
agent-prompt-worker-fork-execution.md (2.1.71 → 2.1.86)
data-prompt-caching-design-optimization.md (2.1.83 → 2.1.89)
skill-verify-skill.md (2.1.83 → 2.1.88)
system-prompt-doing-tasks-no-premature-abstractions.md (2.1.53 → 2.1.86)
system-prompt-fork-usage-guidelines.md (2.1.85 → 2.1.88)
system-prompt-git-status.md (2.1.30 → 2.1.88)
system-prompt-writing-subagent-prompts.md (2.1.70 → 2.1.88)
system-reminder-plan-mode-is-active-iterative.md (2.1.81 → 2.1.88)
system-reminder-ultraplan-mode.md (2.1.85 → 2.1.88)
tool-description-agent-usage-notes.md (2.1.84 → 2.1.88)
tool-description-agent-when-to-launch-subagents.md (2.1.84 → 2.1.89)
tool-description-bash-sandbox-tmpdir.md (2.1.53 → 2.1.86)
tool-description-edit.md (2.1.20 → 2.1.86)
tool-description-powershell.md (2.1.84 → 2.1.88)
tool-description-teammatetool.md (2.1.75 → 2.1.88)

New prompt files have been created; either more are now supported by tweakcc or Anthropic has added new ones.
You can now customize the markdown files at /[USER_HOME]/.claude/tweakcc/system-prompts in a text editor.
Then run tweakcc and select "apply" or use tweakcc --apply to update your system prompts

startupCheck: /[USER_HOME]/.claude/tweakcc/cli.js.backup not found; backing up cli.js
backupClijs: Skipping for native installation (no cliPath)
Found Claude Code (native installation): /[USER_HOME]/.local/share/claude/versions/2.1.89
Version: 2.1.89
Loading system prompts...
Applying customizations...
Restoring native binary from backup to /[USER_HOME]/.local/share/claude/versions/2.1.89
[restore] Original file mode for /[USER_HOME]/.local/share/claude/versions/2.1.89: 755
[restore] Unlinked /[USER_HOME]/.local/share/claude/versions/2.1.89 to break hard links
[restore] Restored permissions to 755
Extracting claude.js from backup: /[USER_HOME]/.claude/tweakcc/native-binary.backup
getBunData: Binary format detected as ELF

[ERROR OUTPUT - Technical details included but no correlation IDs or usernames]

Error: Failed to extract claude.js from native installation
at ur (file:///mnt/c/xampp/node_modules/tweakcc/dist/config-ChxM7yMT.mjs:667:10780)
at async Gt (file:///mnt/c/xampp/node_modules/tweakcc/dist/index.mjs:26:133)
at async Command. (file:///mnt/c/xampp/node_modules/tweakcc/dist/index.mjs:24:1708)

Node.js v20.20.0

[matheusmoreira]

I also ran into this issue while trying to patch the system prompts.

$ uname -a
Linux virtdev 6.19.11-arch1-1 #1 SMP PREEMPT_DYNAMIC Thu, 02 Apr 2026 23:33:01 +0000 x86_64 GNU/Linux
$ npx tweakcc@latest --apply --debug
Need to install the following packages:
tweakcc@4.0.11
Ok to proceed? (y) y
Applying saved customizations to Claude Code...
Configuration saved at: /home/dev/.tweakcc/config.json
Reading config at /home/dev/.tweakcc/config.json
getClaudeFromPath: Found claude at /home/dev/.local/bin/claude
Checking claude on PATH: /home/dev/.local/bin/claude
resolvePathToInstallationType: /home/dev/.local/bin/claude -> /home/dev/.local/share/claude/versions/2.1.92
resolvePathToInstallationType: Detected mime type: application/x-executable
extractVersion: Got version 2.1.92 from filename
Using Claude Code from PATH: /home/dev/.local/share/claude/versions/2.1.92 (native-binary, v2.1.92)
startupCheck: /home/dev/.tweakcc/cli.js.backup not found; backing up cli.js
backupClijs: Skipping for native installation (no cliPath)
Found Claude Code (native installation): /home/dev/.local/share/claude/versions/2.1.92
Version: 2.1.92
Loading system prompts...
Applying customizations...
Restoring native binary from backup to /home/dev/.local/share/claude/versions/2.1.92
[restore] Original file mode for /home/dev/.local/share/claude/versions/2.1.92: 755
[restore] Unlinked /home/dev/.local/share/claude/versions/2.1.92 to break hard links
[restore] Restored permissions to 755
Extracting claude.js from backup: /home/dev/.tweakcc/native-binary.backup
getBunData: Binary format detected as ELF
extractClaudeJsFromNativeInstallation: Error during extraction: Error: ELF binary has no overlay data
    at g (file:///home/dev/.npm/_npx/368f197513ec917a/node_modules/tweakcc/dist/nativeInstallation-CyC73KTI.mjs:3:2988)
    at y (file:///home/dev/.npm/_npx/368f197513ec917a/node_modules/tweakcc/dist/nativeInstallation-CyC73KTI.mjs:3:4584)
    at Module.b (file:///home/dev/.npm/_npx/368f197513ec917a/node_modules/tweakcc/dist/nativeInstallation-CyC73KTI.mjs:3:4737)
    at v (file:///home/dev/.npm/_npx/368f197513ec917a/node_modules/tweakcc/dist/config-ChxM7yMT.mjs:1:740)
    at async ur (file:///home/dev/.npm/_npx/368f197513ec917a/node_modules/tweakcc/dist/config-ChxM7yMT.mjs:667:10757)
    at async Gt (file:///home/dev/.npm/_npx/368f197513ec917a/node_modules/tweakcc/dist/index.mjs:26:133)
    at async Command.<anonymous> (file:///home/dev/.npm/_npx/368f197513ec917a/node_modules/tweakcc/dist/index.mjs:24:1708)
file:///home/dev/.npm/_npx/368f197513ec917a/node_modules/tweakcc/dist/config-ChxM7yMT.mjs:667
`)},I=(e,t,n)=>{let r=[],i=t.global?t:new RegExp(t.source,t.flags+`g`), ...

... lots of code ...

... &&(console.warn(e.yellow(`












Error: Failed to extract claude.js from native installation
    at ur (file:///home/dev/.npm/_npx/368f197513ec917a/node_modules/tweakcc/dist/config-ChxM7yMT.mjs:667:10780)
    at async Gt (file:///home/dev/.npm/_npx/368f197513ec917a/node_modules/tweakcc/dist/index.mjs:26:133)
    at async Command.<anonymous> (file:///home/dev/.npm/_npx/368f197513ec917a/node_modules/tweakcc/dist/index.mjs:24:1708)

Node.js v25.9.0

[imdeveloper01]

Is this fixable?

[2233admin]

Different but related scenario on Windows: npm installed first, native installed later — tweakcc silently keeps patching the wrong target.

Setup:

• CC originally installed via npm → tweakcc configured, ccInstallationPath cached to npm cli.js
• Later, CC migrated to native Windows installer (~/.local/bin/claude.exe)
• /doctor shows: Currently running: native, Warning: Leftover npm global installation
• tweakcc never re-detects: still patches npm cli.js, native exe runs unpatched

No error, no warning — tweakcc happily reports success but all patches go to the wrong install. Silent failure.

Root cause: tweakcc caches ccInstallationPath and never re-validates it against what's actually on PATH/running.

Workaround:

tweakcc unpack C:/tmp/claude-cli.js C:/Users/<user>/.local/bin/claude.exe
# manually update ccInstallationPath in ~/.tweakcc/config.json to C:/tmp/claude-cli.js
tweakcc --apply
tweakcc repack C:/tmp/claude-cli.js C:/Users/<user>/.local/bin/claude.exe  # requires CC to be closed

Suggested fix: On startup, compare ccInstallationPath version against the claude binary on PATH. If they differ, warn and offer to re-detect.

[imdeveloper01]

Different but related scenario on Windows: npm installed first, native installed later — tweakcc silently keeps patching the wrong target.

Setup:

• CC originally installed via npm → tweakcc configured, ccInstallationPath cached to npm cli.js
• Later, CC migrated to native Windows installer (~/.local/bin/claude.exe)
• /doctor shows: Currently running: native, Warning: Leftover npm global installation
• tweakcc never re-detects: still patches npm cli.js, native exe runs unpatched

No error, no warning — tweakcc happily reports success but all patches go to the wrong install. Silent failure.

Root cause: tweakcc caches ccInstallationPath and never re-validates it against what's actually on PATH/running.

Workaround:

tweakcc unpack C:/tmp/claude-cli.js C:/Users//.local/bin/claude.exe

manually update ccInstallationPath in ~/.tweakcc/config.json to C:/tmp/claude-cli.js

tweakcc --apply
tweakcc repack C:/tmp/claude-cli.js C:/Users//.local/bin/claude.exe # requires CC to be closed
Suggested fix: On startup, compare ccInstallationPath version against the claude binary on PATH. If they differ, warn and offer to re-detect.

This is essentially overwriting the native .exe with a patched one, right?

[SoftwareGuy]

Can confirm, having this issue on a installed copy of 2.1.94, 2.1.92. Downgraded to 2.1.80 and patches work. It's related to the Bun ELF format change it seems.

[imdeveloper01]

Is there a fork that has this issue resolved?

[bl-ue]

@imdeveloper01 @SoftwareGuy @2233admin @viceversaco @matheusmoreira I'm sorry for the lack of responses to these issues! We've been very busy with Piebald feedback for the past couple weeks and haven't had much spare time for our opensource work. We'll clear the backlog on tweakcc this week.

[SoftwareGuy]

I'm sorry for the lack of responses to these issues! We've been very busy with Piebald feedback for the past couple weeks and haven't had much spare time for our opensource work. We'll clear the backlog on tweakcc this week.

Thanks for letting us know. 😄
Looking forward to getting this fixed for the versions that are having problems applying the tweaks. Been looking at the fixes on 2.1.80 and they've been working pretty well.