Always update connections.env and fix double-toggled connection line

Drop the --legacy flag: set_local_db and toggle_index now run
unconditionally instead of only when -l was passed, since that was the
flag's only effect.

Fix set_dot_env writing the connection/RCC_CONNECTION line twice with
opposing polarity (once from the #docker pass, once from the #cidb
pass), which flipped it to the wrong value. Collapsed the three
separate open/read/write passes into one, toggling both sections and
the connection line in a single scan so the connection line is only
ever touched once.

src/arguments.rs

@@ -13,13 +13,6 @@ pub struct Arguments {
 
     #[arg(help = "Possible values are 'up' and 'down'")]
     pub action: String,
-
-    #[arg(
-        short = 'l',
-        long = "legacy",
-        help = "Legacy mode for old env reading."
-    )]
-    pub legacy: bool,
 }
 
 impl Arguments {
@@ -40,7 +33,6 @@ mod tests {
         Arguments {
             project: "test".to_string(),
             action: action.to_string(),
-            legacy: false,
         }
     }