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ALE automatically loads all available linters and LSP clients for the filetype so, if ccls is correctly installed, it should work out-of-the-box. Moreover, ALE will automatically detect the root folder of your project.
To set init options for ccls, add to ~/.vimrc or ~/.vim/vimrc (example for cpp files, set other filetypes as needed):
Diagnostic is enabled out-of-the-box. Completion (omnifunc) can be enabled with:
letg:ale_completion_enabled=1
ALE also provides a completion source for deoplete, which should work out-of-the-box if deoplete is installed and enabled.
ALE exposes commands to invoke LSP features (see |ale|):
" Example keybindingsnn<silent><M-d>:ALEGoToDefinition<cr>nn<silent><M-r>:ALEFindReferences<cr>nn<silent><M-a>:ALESymbolSearch<cr>nn<silent><M-h>:ALEHover<cr>