Revert "use 3-way merge when applying user changes"

this is still not robust enough to cover the scenario where the user
deleted a file.

we should just do a hard reset to the environment's changes instead, and
not attempt to restore their changes, since we just synced them over.

This reverts commit 856d418.

Author: vito

repository/repository.go

@@ -471,30 +471,13 @@ func (r *Repository) Apply(ctx context.Context, id string, w io.Writer) (rerr er
 	if hasUnstagedChanges {
 		fmt.Fprintf(w, "Restoring user changes...\n")
 
-		// 1. Temporarily commit the agent's changes (if any)
-		if err := RunInteractiveGitCommand(ctx, r.userRepoPath, w,
-			"commit",
-			// it's simpler/safer to just keep this path unconditional than check if there
-			// were staged stuff before, so just allow an empty commit; we'll be
-			// getting rid of it immediately anyway
-			"--allow-empty",
-			"-m", "temp: agent changes (you should not see this)",
-		); err != nil {
+		// 1. Temporarily commit the agent's changes
+		if err := RunInteractiveGitCommand(ctx, r.userRepoPath, w, "commit", "-m", "temp: agent changes"); err != nil {
 			return fmt.Errorf("failed to commit agent changes: %w", err)
 		}
 
-		// 2. Apply the user's patch, using 3-way merge with --check beforehand to
-		// avoid leaving conflict markers
-		var checkOut strings.Builder
-		checkCmd := exec.CommandContext(ctx, "git", "apply", "--3way", "--check", "-")
-		checkCmd.Dir = r.userRepoPath
-		checkCmd.Stdin = strings.NewReader(diffOutput)
-		checkCmd.Stdout = &checkOut
-		checkCmd.Stderr = &checkOut
-		if err := checkCmd.Run(); err != nil {
-			return fmt.Errorf("conflict detected when re-applying user changes:\n%s", checkOut.String())
-		}
-		applyCmd := exec.CommandContext(ctx, "git", "apply", "--3way", "-")
+		// 2. Apply the user's patch
+		applyCmd := exec.CommandContext(ctx, "git", "apply", "-")
 		applyCmd.Dir = r.userRepoPath
 		applyCmd.Stdin = strings.NewReader(diffOutput)
 		applyCmd.Stdout = w