diff --git a/cli/src/commands/cancel.zig b/cli/src/commands/cancel.zig
index 1217a89..e33ed58 100644
--- a/cli/src/commands/cancel.zig
+++ b/cli/src/commands/cancel.zig
@@ -11,8 +11,8 @@ const manifest_lib = @import("../manifest.zig");
 pub fn run(allocator: std.mem.Allocator, args: []const []const u8) !void {
     var flags = core.flags.CommonFlags{};
     var force = false;
-    var targets = std.ArrayList([]const u8).init(allocator);
-    defer targets.deinit();
+    var targets: std.ArrayList([]const u8) = .empty;
+    defer targets.deinit(allocator);
 
     // Parse arguments
     var i: usize = 0;
@@ -28,7 +28,7 @@ pub fn run(allocator: std.mem.Allocator, args: []const []const u8) !void {
             core.output.errorMsg("cancel", "Unknown option");
             return error.InvalidArgs;
         } else {
-            try targets.append(arg);
+            try targets.append(allocator, arg);
         }
     }
 
@@ -129,7 +129,7 @@ fn cancelLocal(allocator: std.mem.Allocator, run_id: []const u8, force: bool, js
 
     if (!force) {
         // Wait 5 seconds for graceful termination
-        std.time.sleep(5 * std.time.ns_per_s);
+        std.Thread.sleep(5 * std.time.ns_per_s);
     }
 
     // Check if still running, send SIGKILL if needed
@@ -170,7 +170,7 @@ fn cancelLocal(allocator: std.mem.Allocator, run_id: []const u8, force: bool, js
 /// Check if process is still running
 fn isProcessRunning(pid: i32) bool {
     const result = std.posix.kill(pid, 0);
-    return result == error.PermissionDenied or result == {};
+    return if (result) |_| true else |err| err == error.PermissionDenied;
 }
 
 /// Cancel server job
diff --git a/cli/src/commands/log.zig b/cli/src/commands/log.zig
index 4b7a0c1..8eec012 100644
--- a/cli/src/commands/log.zig
+++ b/cli/src/commands/log.zig
@@ -12,7 +12,7 @@ const crypto = @import("../utils/crypto.zig");
 /// Usage:
 ///   ml logs <run_id>              # Fetch logs from local file or server
 ///   ml logs <run_id> --follow     # Stream logs from server
-pub fn execute(allocator: std.mem.Allocator, args: []const []const u8) !void {
+pub fn run(allocator: std.mem.Allocator, args: []const []const u8) !void {
     var flags = core.flags.CommonFlags{};
     var command_args = try core.flags.parseCommon(allocator, args, &flags);
     defer command_args.deinit(allocator);
@@ -68,7 +68,7 @@ fn fetchLocalLogs(allocator: std.mem.Allocator, target: []const u8, cfg: *const
     defer allocator.free(manifest_path);
 
     // Read manifest to get artifact path
-    const manifest = try manifest_lib.readManifest(manifest_path, allocator);
+    var manifest = try manifest_lib.readManifest(manifest_path, allocator);
     defer manifest.deinit(allocator);
 
     // Build output.log path
@@ -90,8 +90,8 @@ fn fetchLocalLogs(allocator: std.mem.Allocator, target: []const u8, cfg: *const
 
     if (json) {
         // Escape content for JSON
-        var escaped = std.ArrayList(u8).init(allocator);
-        defer escaped.deinit();
+        var escaped: std.ArrayList(u8) = .empty;
+        defer escaped.deinit(allocator);
         const writer = escaped.writer(allocator);
 
         for (content) |c| {
@@ -130,7 +130,7 @@ fn fetchServerLogs(allocator: std.mem.Allocator, target: []const u8, cfg: config
     var client = try ws.Client.connect(allocator, ws_url, cfg.api_key);
     defer client.close();
 
-    try client.sendFetchLogs(target, api_key_hash);
+    try client.sendGetLogs(target, api_key_hash);
 
     const message = try client.receiveMessage(allocator);
     defer allocator.free(message);
diff --git a/cli/src/commands/run.zig b/cli/src/commands/run.zig
index 7d79a0f..7716ca3 100644
--- a/cli/src/commands/run.zig
+++ b/cli/src/commands/run.zig
@@ -1,9 +1,29 @@
 const std = @import("std");
-const config = @import("../config.zig");
 const db = @import("../db.zig");
-const core = @import("../core.zig");
-const colors = @import("../utils/colors.zig");
 const manifest_lib = @import("../manifest.zig");
+const colors = @import("../utils/colors.zig");
+const core = @import("../core.zig");
+const config = @import("../config.zig");
+
+extern fn execvp(path: [*:0]const u8, argv: [*]const ?[*:0]const u8) c_int;
+extern fn waitpid(pid: c_int, status: *c_int, flags: c_int) c_int;
+
+// Get current environment from libc
+extern var environ: [*]const ?[*:0]const u8;
+
+// Inline macros for wait status parsing (not available as extern on macOS)
+fn WIFEXITED(status: c_int) c_int {
+    return if ((status & 0x7F) == 0) 1 else 0;
+}
+fn WEXITSTATUS(status: c_int) c_int {
+    return (status >> 8) & 0xFF;
+}
+fn WIFSIGNALED(status: c_int) c_int {
+    return if (((status & 0x7F) != 0x7F) and ((status & 0x7F) != 0)) 1 else 0;
+}
+fn WTERMSIG(status: c_int) c_int {
+    return status & 0x7F;
+}
 const Manifest = manifest_lib.RunManifest;
 
 /// Run command - always executes locally
@@ -97,7 +117,7 @@ pub fn execute(allocator: std.mem.Allocator, args: []const []const u8) !void {
     _ = try db.DB.step(stmt);
 
     // Write manifest
-    try manifest_lib.writeManifest(manifest, manifest_path);
+    try manifest_lib.writeManifest(manifest, manifest_path, allocator);
 
     // Fork and execute
     const output_log_path = try std.fs.path.join(allocator, &[_][]const u8{
@@ -176,22 +196,22 @@ fn resolveCommand(allocator: std.mem.Allocator, cfg: *const config.Config, args:
     if (cfg.experiment) |exp| {
         if (exp.entrypoint.len > 0) {
             // Split entrypoint on spaces
-            var argv = std.ArrayList([]const u8).init(allocator);
+            var argv: std.ArrayList([]const u8) = .empty;
 
             // Parse entrypoint (split on spaces)
             var iter = std.mem.splitScalar(u8, exp.entrypoint, ' ');
             while (iter.next()) |part| {
                 if (part.len > 0) {
-                    try argv.append(try allocator.dupe(u8, part));
+                    try argv.append(allocator, try allocator.dupe(u8, part));
                 }
             }
 
             // Append args
             for (args) |arg| {
-                try argv.append(try allocator.dupe(u8, arg));
+                try argv.append(allocator, try allocator.dupe(u8, arg));
             }
 
-            return argv.toOwnedSlice();
+            return try argv.toOwnedSlice(allocator);
         }
     }
 
@@ -246,7 +266,6 @@ fn executeAndCapture(
     // Create output file
     var output_file = try std.fs.cwd().createFile(output_path, .{});
     defer output_file.close();
-    const output_writer = output_file.writer();
 
     // Create pipe for stdout
     const pipe = try std.posix.pipe();
@@ -263,13 +282,13 @@ fn executeAndCapture(
         std.posix.close(pipe[0]); // Close read end
 
         // Redirect stdout to pipe
-        _ = std.posix.dup2(pipe[1], std.posix.STDOUT_FILENO);
-        _ = std.posix.dup2(pipe[1], std.posix.STDERR_FILENO);
+        _ = std.posix.dup2(pipe[1], std.posix.STDOUT_FILENO) catch std.process.exit(1);
+        _ = std.posix.dup2(pipe[1], std.posix.STDERR_FILENO) catch std.process.exit(1);
         std.posix.close(pipe[1]);
 
-        // Execute command
-        const err = std.posix.execvpe(command[0], command, &[_:null]?[*:0]const u8{null});
-        std.log.err("Failed to execute {s}: {}", .{ command[0], err });
+        // Execute command using execvp (uses current environ)
+        const c_err = execvp(@ptrCast(command[0].ptr), @ptrCast(command.ptr));
+        std.log.err("Failed to execute {s}: {}", .{ command[0], c_err });
         std.process.exit(1);
         unreachable;
     }
@@ -299,7 +318,7 @@ fn executeAndCapture(
         if (bytes_read == 0) break;
 
         // Write to output file
-        try output_writer.writeAll(buf[0..bytes_read]);
+        try output_file.writeAll(buf[0..bytes_read]);
 
         // Parse lines
         for (buf[0..bytes_read]) |byte| {
@@ -318,14 +337,14 @@ fn executeAndCapture(
     }
 
     // Wait for child
-    var status: u32 = 0;
-    _ = std.posix.waitpid(pid, &status, 0);
+    var status: c_int = 0;
+    _ = waitpid(@intCast(pid), &status, 0);
 
     // Parse exit code
-    if (std.os.linux.W.IFEXITED(status)) {
-        return std.os.linux.W.EXITSTATUS(status);
-    } else if (std.os.linux.W.IFSIGNALED(status)) {
-        return 128 + std.os.linux.W.TERMSIG(status);
+    if (WIFEXITED(status) != 0) {
+        return WEXITSTATUS(status);
+    } else if (WIFSIGNALED(status) != 0) {
+        return 128 + WTERMSIG(status);
     }
 
     return -1;
diff --git a/cli/src/native/hash.zig b/cli/src/native/hash.zig
index 59835f5..c619dae 100644
--- a/cli/src/native/hash.zig
+++ b/cli/src/native/hash.zig
@@ -12,17 +12,17 @@ pub const HashError = error{
 
 // Global context for reuse across multiple hash operations
 var global_ctx: ?*c.fh_context_t = null;
-var ctx_initialized = std.atomic.Atomic(bool).init(false);
+var ctx_initialized = std.atomic.Value(bool).init(false);
 var init_mutex = std.Thread.Mutex{};
 
 /// Initialize global hash context once (thread-safe)
 pub fn init() !void {
-    if (ctx_initialized.load(.Acquire)) return;
+    if (ctx_initialized.load(.seq_cst)) return;
 
     init_mutex.lock();
     defer init_mutex.unlock();
 
-    if (ctx_initialized.load(.Relaxed)) return; // Double-check
+    if (ctx_initialized.load(.seq_cst)) return; // Double-check
 
     const start = std.time.milliTimestamp();
     global_ctx = c.fh_init(0); // 0 = auto-detect threads
@@ -32,7 +32,7 @@ pub fn init() !void {
         return HashError.ContextInitFailed;
     }
 
-    ctx_initialized.store(true, .Release);
+    ctx_initialized.store(true, .seq_cst);
     std.log.info("[native] hash context initialized: {}ms", .{elapsed});
 }
 
diff --git a/cli/src/utils/parallel_walk.zig b/cli/src/utils/parallel_walk.zig
index 68cc964..917fd24 100644
--- a/cli/src/utils/parallel_walk.zig
+++ b/cli/src/utils/parallel_walk.zig
@@ -15,7 +15,7 @@ const WorkQueue = struct {
 
     fn init(allocator: std.mem.Allocator) WorkQueue {
         return .{
-            .items = std.ArrayList(WorkItem).init(allocator),
+            .items = .empty,
             .mutex = .{},
             .condition = .{},
             .done = false,