Finished code cleanup, readme is mostly done.

cmd/main.go

@@ -16,6 +16,9 @@ import (
 	"os"
 )
 
+// main is the entry point to the application. It's mostly responsible for bootstrapping the database, configuration,
+// logging, and llms. It passes everything to subcommands by injecting state into the context to avoid coupling during
+// initialization.
 func main() {
 	app := &cli.Command{
 		Name:  "ai-coding-assistant",
@@ -60,6 +63,7 @@ func main() {
 	}
 }
 
+// readConfig attempts to read the configuration file.
 func readConfig(ctx context.Context, cmd *cli.Command) (context.Context, error) {
 	cfgFile := cmd.String("config")
 	cfgHandle, err := os.Open(cfgFile)