I want to share my experience with this case.
Ansible from 2.2 is had with_filetree loop provides simple way to upload dirs, links, static files and even (!) templates. It's best way to keep my config dir synchronized.
- name: etc config - Create directories
  file:
    path: "{{ nginx_conf_dir }}/{{ item.path }}"
    state: directory
    mode: 0755
  with_filetree: etc/nginx
  when: item.state == 'directory'
- name: etc config - Creating configuration files from templates
  template:
    src: "{{ item.src }}"
    dest: "{{ nginx_conf_dir }}/{{ item.path | regex_replace('\\.j2$', '') }}"
    mode: 0644
  with_filetree: etc/nginx
  when:
    - item.state == "file"
    - item.path | match('.+\.j2$') | bool
- name: etc config - Creating staic configuration files
  copy:
    src: "{{ item.src }}"
    dest: "{{ nginx_conf_dir }}/{{ item.path }}"
    mode: 0644
  with_filetree: etc/nginx
  when:
    - item.state == "file"
    - not (item.path | match('.+\.j2$') | bool)
- name: etc config - Recreate symlinks
  file:
    src: "{{ item.src }}"
    dest: "{{ nginx_conf_dir }}/{{ item.path }}"
    state: link
    force: yes
    mode: "{{ item.mode }}"
  with_filetree: etc/nginx
  when: item.state == "link"
Next we may want delete unused files from config dir. It's simple.
We gather list of uploaded files and files exist on remote server, next remove diffrence.
But we may want to have unmanaged files in config dir.
I've used -prune functionality of find to avoid clearing folders with unmanaged files.
PS _(Y)_ sure after I have deleted some unmanaged files
- name: etc config - Gathering managed files
  set_fact:
    __managed_file_path: "{{ nginx_conf_dir }}/{{ item.path | regex_replace('\\.j2$', '') }}"
  with_filetree: etc/nginx
  register: __managed_files
- name: etc config - Convert managed files to list
  set_fact: managed_files="{{ __managed_files.results | map(attribute='ansible_facts.__managed_file_path') | list }}"
- name: etc config - Gathering exist files (excluding .ansible_keep-content dirs)
  shell: find /etc/nginx -mindepth 1 -type d -exec test -e '{}/.ansible_keep-content' \; -prune -o -print
  register: exist_files
  changed_when: False
- name: etc config - Delete unmanaged files
  file: path="{{ item }}" state=absent
  with_items: "{{ exist_files.stdout_lines }}"
  when:
    - item not in managed_files