Is there a way for extracting only the relevant files web site files

I need to deploy my site to embedded system and I need it to be small as it can be. My site folder structure is:

• sitename
  • favicon.ico
  • index.html
  • application (my files, need all of them)
    • css
    • js
  • fontawesome (library, need only some file)
    • css
    • js
    • less
    • metadata
    • more folders below
  • kendoui (library, need only some file)
    • apptemplates
    • examples
    • js
    • license-agreements
    • src
    • styles
    • more folders below

Is there a way / tool to export only the needed file while maintaining the folder structure?