Fix LSP and update plugins

- Structure LSP configuration code
- Since `lsp-zero` is deprecated, instead use `nvim-lspconfig`
- Use `nvim_lsp_signature_help` instead of `lsp_signature`

nvim/lua/lsp/pylsp.lua

@@ -0,0 +1,4 @@
+lsp.config('pylsp', {
+    capabilities = cmp_defcaps,
+})
+lsp.enable('pylsp')