refactor(build): update user directory structure and Makefile paths

- Move user command sources from user/ to user/cmd/ directory
- Update Makefile to reference user/cmd/ path for compiling .c files
- Restructure user/ directory to separate commands from runtime components
- Add documentation about cmd/ and runtime/ organization in user/README.md
- Update main README.md to reflect new user space structure
- Maintain existing

examples/typephp-os/Makefile

@@ -116,7 +116,7 @@ $(BOOTSTRAP_OBJECT): boot/boot.S | $(OBJECT_DIR)
 $(KERNEL64_ENTRY_OBJECT): boot/kernel64-entry.S | $(OBJECT_DIR)
 	gcc $(KERNEL64_BOOTFLAGS) -c $< -o $@
 
-$(OBJECT_DIR)/%.o: user/%.c $(USER_HEADERS) kernel/core/abi/typephp_os_syscall.h | $(OBJECT_DIR)
+$(OBJECT_DIR)/%.o: user/cmd/%.c $(USER_HEADERS) kernel/core/abi/typephp_os_syscall.h | $(OBJECT_DIR)
 	gcc $(USER_CFLAGS) -c $< -o $@
 
 $(OPENLIBM_SOURCES): | thirdparty

examples/typephp-os/README.md

@@ -22,7 +22,7 @@ boot/                 Make-built startup assembly and linker scripts
 kernel/*.php          TypePHP kernel implementation
 kernel/core/          Native kernel implementation compiled by tpc
 kernel/core/abi/      Freestanding C/POSIX and C++ compatibility boundary
-user/                 Independently built Ring-3 programs and bootstrap libc
+user/                 Ring-3 commands, TypePHP projects, headers, and runtime
 ```
 
 Additional TypePHP kernel files stay directly under `kernel/` until a concrete

examples/typephp-os/user/README.md

@@ -33,6 +33,10 @@ The following rules are normative for this directory:
    programs must link the same `libtypephp-os.a` platform runtime instead of
    maintaining private startup or libc copies.
 
+The resident shell and its standalone C command sources live under `cmd/`.
+Reusable startup, syscall, POSIX/libc, C++ ABI, and math support lives under
+`runtime/` and is emitted only as `build/libtypephp-os.a`.
+
 The current shared userspace runtime provides `syscall`, `read`, `write`, `openat`,
 `open`, `close`, `lseek`, `getcwd`, `chdir`, `mkdir`, `rmdir`, `unlink`,
 `rename`, `stat`, `lstat`, `fstat`, `access`, `fsync`, `fdatasync`, `truncate`,