Replace git worktrees with local clones for session isolation

Session isolation now uses git clone --local instead of worktrees.
Clones stored in ~/.clave/repos/ instead of project .clave/wt/.
Renamed CreateWorktree to CloneRepo and updated GitManager methods:
createWorktree → cloneLocal, removeWorktree → removeClone,
mergeAndCleanWorktree → mergeAndCleanClone.
Updated SessionContext properties: worktree_path → clone_path,
worktree_branch → clone_branch.

Author: inxilpro

CLAUDE.md

@@ -4,7 +4,7 @@ This file provides guidance to Claude Code (claude.ai/code) when working with co
 
 ## Project Overview
 
-Clave is a Laravel Zero CLI that spins up ephemeral Ubuntu VMs via [Tart](https://tart.run/) for isolated Claude Code sessions against Laravel projects. Run `clave` from within a Laravel project's git repo — it handles worktree creation, VM lifecycle, networking, and teardown automatically. Multiple simultaneous sessions work naturally with unique worktrees, VMs, and ports.
+Clave is a Laravel Zero CLI that spins up ephemeral Ubuntu VMs via [Tart](https://tart.run/) for isolated Claude Code sessions against Laravel projects. Run `clave` from within a Laravel project's git repo — it handles repo cloning, VM lifecycle, networking, and teardown automatically. Multiple simultaneous sessions work naturally with unique clones, VMs, and ports.
 
 ## Commands
 
@@ -36,7 +36,7 @@ php clave app:build
 
 A `SessionContext` DTO flows through pipeline stages in `DefaultCommand`:
 
-`CreateWorktree → CloneVm → BootVm → RunClaudeCode`
+`CloneRepo → CloneVm → BootVm → RunClaudeCode`
 
 Each stage populates fields on `SessionContext` and calls `$next()`. Teardown runs via `SessionTeardown` in both a `finally` block and SIGINT/SIGTERM signal handler.
 
@@ -45,17 +45,17 @@ Future stages (not yet implemented): `DiscoverGateway → CreateSshTunnel → Co
 ### Key Services (all registered as singletons)
 
 - **TartManager** — wraps the `tart` CLI for VM clone/run/stop/delete/ip
-- **GitManager** — worktree create/remove/merge, .gitignore management
+- **GitManager** — local clone/remove/merge for session isolation
 - **SshExecutor** — SSH command execution, tunnels, interactive TTY sessions
 - **HerdManager** — Herd Pro proxy/unproxy (future use)
 - **SessionTeardown** — reverses each pipeline stage on exit
 - **ProvisioningPipeline** — generates bash provisioning script for base VM setup
 
 ### DTOs
 
-- **SessionContext** — mutable pipeline state (session_id, vm_name, vm_ip, worktree_path, etc.)
+- **SessionContext** — mutable pipeline state (session_id, vm_name, vm_ip, clone_path, etc.)
 - **ServiceConfig** — readonly database/Redis config
-- **OnExit** — enum (Keep, Merge, Discard) for worktree handling on session end
+- **OnExit** — enum (Keep, Merge, Discard) for clone handling on session end
 
 ## Conventions
 

PLAN.md

@@ -15,7 +15,7 @@ A Laravel Zero CLI that spins up ephemeral Ubuntu VMs via Tart for isolated Clau
 - [x] `ProvisionCommand` + `ProvisioningPipeline` — build base image (PHP 8.4, nginx, Node 22, Claude Code)
 - [x] `AuthManager` + `AuthCommand` — API key + OAuth token support with local storage
 - [x] Preflight pipeline: `ValidateProject → GetGitBranch → EnsureVmExists → CheckClaudeAuthentication → SaveSession`
-- [x] Session pipeline: `CreateWorktree → CloneVm → BootVm → RunClaudeCode`
+- [x] Session pipeline: `CloneRepo → CloneVm → BootVm → RunClaudeCode`
 - [x] `SessionTeardown` — VM stop/delete, worktree prompt, Herd unproxy, tunnel kill, session record cleanup
 - [x] Signal handling via `$this->trap()` (SIGINT/SIGTERM)
 - [x] Sessions SQLite table + `Session` model
@@ -208,8 +208,8 @@ class SessionContext
         public ?string $base_branch = null,
         public ?string $vm_name = null,
         public ?string $vm_ip = null,
-        public ?string $worktree_path = null,
-        public ?string $worktree_branch = null,
+        public ?string $clone_path = null,
+        public ?string $clone_branch = null,
         public ?string $proxy_name = null,
         public ?int $tunnel_port = null,
         public ?InvokedProcess $tunnel_process = null,
@@ -296,31 +296,31 @@ ValidateProject → GetGitBranch → EnsureVmExists → CheckClaudeAuthenticatio
 Label: "Starting session..."
 
 ```
-CreateWorktree → CloneVm → BootVm → RunClaudeCode
+CloneRepo → CloneVm → BootVm → RunClaudeCode
 ```
 
 Future stages to be inserted between `BootVm` and `RunClaudeCode`:
 ```
 DiscoverGateway → CreateSshTunnel → ConfigureHerdProxy → BootstrapLaravel
 ```
 
-#### CreateWorktree
+#### CloneRepo
 
 ```php
-class CreateWorktree implements Step, ProgressAware
+class CloneRepo implements Step, ProgressAware
 {
     use AcceptsProgress;
 
     public function handle(SessionContext $context, Closure $next): mixed
     {
         $branch = "clave/s-{$context->session_id}";
-        $worktree_path = "{$context->project_dir}/.clave/wt/s-{$context->session_id}";
+        $clone_path = "{$context->project_dir}/.clave/wt/s-{$context->session_id}";
 
         $this->git->ensureIgnored($context->project_dir, '.clave/');
-        $this->git->createWorktree($context->project_dir, $worktree_path, $branch);
+        $this->git->cloneLocal($context->project_dir, $clone_path, $branch);
 
-        $context->worktree_path = $worktree_path;
-        $context->worktree_branch = $branch;
+        $context->clone_path = $clone_path;
+        $context->clone_branch = $branch;
 
         return $next($context);
     }
@@ -364,7 +364,7 @@ class BootVm implements Step, ProgressAware
 
     public function handle(SessionContext $context, Closure $next): mixed
     {
-        $mount_path = $context->worktree_path ?? $context->project_dir;
+        $mount_path = $context->clone_path ?? $context->project_dir;
 
         $this->tart->runBackground($context->vm_name, [
             'project' => $mount_path,
@@ -495,11 +495,11 @@ class SessionTeardown
         $this->killTunnel($context);     // Stop SSH tunnel if running
         $this->stopVm($context);         // tart stop
         $this->deleteVm($context);       // tart delete
-        $this->handleWorktree($context); // Prompt: keep/merge/discard
+        $this->handleClone($context); // Prompt: keep/merge/discard
         $this->deleteSession($context);  // Remove Session record
     }
 
-    protected function handleWorktree(SessionContext $context): void
+    protected function handleClone(SessionContext $context): void
     {
         $action = $context->on_exit;
 
@@ -511,8 +511,8 @@ class SessionTeardown
         ));
 
         match ($action) {
-            OnExit::Merge => $this->git->mergeAndCleanWorktree(...),
-            OnExit::Discard => $this->git->removeWorktree(...),
+            OnExit::Merge => $this->git->mergeAndCleanClone(...),
+            OnExit::Discard => $this->git->removeClone(...),
             default => null, // keep
         };
     }
@@ -697,9 +697,9 @@ class GitManager
 {
     public function isRepo(string $path): bool;
     public function currentBranch(string $path): string;
-    public function createWorktree(string $repo_path, string $worktree_path, string $branch): void;
-    public function removeWorktree(string $repo_path, string $worktree_path): void;
-    public function mergeAndCleanWorktree(string $repo_path, string $worktree_path, string $branch, string $target): void;
+    public function cloneLocal(string $repo_path, string $clone_path, string $branch): void;
+    public function removeClone(string $repo_path, string $clone_path): void;
+    public function mergeAndCleanClone(string $repo_path, string $clone_path, string $branch, string $target): void;
     public function ensureIgnored(string $repo_path, string $pattern): void;
 }
 ```
@@ -820,7 +820,7 @@ clave/
 │   │   │   ├── EnsureVmExists.php
 │   │   │   ├── CheckClaudeAuthentication.php
 │   │   │   ├── SaveSession.php
-│   │   │   ├── CreateWorktree.php
+│   │   │   ├── CloneRepo.php
 │   │   │   ├── CloneVm.php
 │   │   │   ├── BootVm.php
 │   │   │   └── RunClaudeCode.php
@@ -873,7 +873,7 @@ Proves the core lifecycle: boot a VM, get a Claude Code session, tear it down.
 6. `ProvisionCommand` + `ProvisioningPipeline` — build base image (PHP 8.4/nginx/Node 22/Claude Code)
 7. `SessionPipeline` base class with progress tracking
 8. Preflight pipeline: `ValidateProject → GetGitBranch → EnsureVmExists → CheckClaudeAuthentication → SaveSession`
-9. Session pipeline: `CreateWorktree → CloneVm → BootVm → RunClaudeCode`
+9. Session pipeline: `CloneRepo → CloneVm → BootVm → RunClaudeCode`
 10. `SessionTeardown` — cleanup VM, worktree prompt, session record
 11. Signal handling via `$this->trap()` (SIGINT/SIGTERM)
 12. Sessions SQLite table + model

app/Data/OnExit.php

@@ -16,7 +16,7 @@ enum OnExit: string
 	public function label(): string
 	{
 		return match ($this) {
-			OnExit::Keep => 'Keep worktree',
+			OnExit::Keep => 'Keep clone',
 			OnExit::Merge => 'Merge and clean up',
 			OnExit::Discard => 'Discard changes',
 			default => Str::headline($this->name),

app/Data/SessionContext.php

@@ -15,9 +15,9 @@ class SessionContext
 
 	public ?string $vm_ip = null;
 
-	public ?string $worktree_path = null;
+	public ?string $clone_path = null;
 
-	public ?string $worktree_branch = null;
+	public ?string $clone_branch = null;
 
 	public ?string $proxy_name = null;
 

app/Pipelines/ClaudeCodePipeline.php

@@ -4,7 +4,7 @@
 
 use App\Pipelines\Steps\BootVm;
 use App\Pipelines\Steps\CloneVm;
-use App\Pipelines\Steps\CreateWorktree;
+use App\Pipelines\Steps\CloneRepo;
 use App\Pipelines\Steps\RunClaudeCode;
 
 class ClaudeCodePipeline extends SessionPipeline
@@ -17,7 +17,7 @@ protected function label(): string
 	protected function steps(): array
 	{
 		return [
-			CreateWorktree::class,
+			CloneRepo::class,
 			CloneVm::class,
 			BootVm::class,
 			RunClaudeCode::class,

app/Pipelines/Steps/BootVm.php

@@ -22,7 +22,7 @@ public function __construct(
 
 	public function handle(SessionContext $context, Closure $next): mixed
 	{
-		$mount_path = $context->worktree_path ?? $context->project_dir;
+		$mount_path = $context->clone_path ?? $context->project_dir;
 
 		$this->hint("Booting VM '{$context->vm_name}'...");
 		$this->tart->runBackground($context->vm_name, [$mount_path]);

app/Pipelines/Steps/CloneRepo.php

@@ -0,0 +1,35 @@
+<?php
+
+namespace App\Pipelines\Steps;
+
+use App\Data\SessionContext;
+use App\Support\GitManager;
+use Closure;
+
+class CloneRepo implements Step, ProgressAware
+{
+	use AcceptsProgress;
+
+	public function __construct(protected GitManager $git)
+	{
+	}
+
+	public function handle(SessionContext $context, Closure $next): mixed
+	{
+		$clone_branch = "clave/s-{$context->session_id}";
+		$clone_path = $this->cloneBasePath().'/s-'.$context->session_id;
+
+		$this->hint('Cloning repo for session...');
+		$this->git->cloneLocal($context->project_dir, $clone_path, $context->base_branch, $clone_branch);
+
+		$context->clone_path = $clone_path;
+		$context->clone_branch = $clone_branch;
+
+		return $next($context);
+	}
+
+	protected function cloneBasePath(): string
+	{
+		return ($_SERVER['HOME'] ?? getenv('HOME')).'/.clave/repos';
+	}
+}

app/Pipelines/Steps/CreateWorktree.php

@@ -23,52 +23,65 @@ public function currentBranch(string $path): string
 		);
 	}
 
-	public function createWorktree(string $repo_path, string $worktree_path, string $branch): mixed
+	public function cloneLocal(string $repo_path, string $clone_path, string $base_branch, string $clone_branch): mixed
 	{
-		$escaped_branch = escapeshellarg($branch);
-		$escaped_path = escapeshellarg($worktree_path);
+		$escaped_path = escapeshellarg($clone_path);
+		$escaped_base = escapeshellarg($base_branch);
+		$escaped_clone = escapeshellarg($clone_branch);
+
+		Process::path($repo_path)
+			->run("git clone --local --branch {$escaped_base} . {$escaped_path}")
+			->throw();
 
-		return Process::path($repo_path)
-			->run("git worktree add -b {$escaped_branch} {$escaped_path}")
+		return Process::path($clone_path)
+			->run("git checkout -b {$escaped_clone}")
 			->throw();
 	}
 
-	public function removeWorktree(string $repo_path, string $worktree_path): mixed
+	public function removeClone(string $clone_path): void
 	{
-		$escaped_path = escapeshellarg($worktree_path);
+		if (is_dir($clone_path)) {
+			Process::run('rm -rf '.escapeshellarg($clone_path));
+		}
+	}
+
+	public function commitAllChanges(string $clone_path, string $message): bool
+	{
+		Process::path($clone_path)->run('git add -A');
+
+		$status = Process::path($clone_path)->run('git status --porcelain');
+
+		if (trim($status->output()) === '') {
+			return false;
+		}
 
-		return Process::path($repo_path)
-			->run("git worktree remove --force {$escaped_path}");
+		Process::path($clone_path)
+			->run('git commit -m '.escapeshellarg($message))
+			->throw();
+
+		return true;
 	}
 
-	public function mergeAndCleanWorktree(string $repo_path, string $worktree_path, string $branch, string $base_branch): void
+	public function mergeAndCleanClone(string $repo_path, string $clone_path, string $clone_branch, string $base_branch): void
 	{
-		$escaped_branch = escapeshellarg($branch);
 		$escaped_base = escapeshellarg($base_branch);
+		$escaped_clone_path = escapeshellarg($clone_path);
+		$escaped_clone_branch = escapeshellarg($clone_branch);
+
+		$this->commitAllChanges($clone_path, 'WIP: auto-commit from clave session');
 
 		Process::path($repo_path)
-			->run("git checkout {$escaped_base}")
+			->run("git fetch {$escaped_clone_path} {$escaped_clone_branch}")
 			->throw();
 
 		Process::path($repo_path)
-			->run("git merge {$escaped_branch}")
+			->run("git checkout {$escaped_base}")
 			->throw();
 
-		$this->removeWorktree($repo_path, $worktree_path);
-
 		Process::path($repo_path)
-			->run("git branch -d {$escaped_branch}");
-	}
-
-	public function ensureIgnored(string $repo_path, string $pattern): void
-	{
-		$gitignore_path = $repo_path.'/.gitignore';
-		$contents = file_exists($gitignore_path) ? file_get_contents($gitignore_path) : '';
-		
-		if (str_contains($contents, $pattern)) {
-			return;
-		}
+			->run('git merge FETCH_HEAD')
+			->throw();
 
-		file_put_contents($gitignore_path, rtrim($contents)."\n{$pattern}\n");
+		$this->removeClone($clone_path);
 	}
 }