Preserve trailing newlines and restore connections.env via git checkout on down

Fix set_local_db/set_dot_env unconditionally stripping (then forcing)
the file's trailing newline: they now detect whether the source file
originally ended in a newline and reproduce that on write, verified
against both the newline and no-newline cases.

Replace the reverse-toggle computation for connections.env on `down`
with a straight `git checkout`, so the file always ends up
byte-for-byte identical to HEAD instead of relying on toggle logic to
get it exactly right. Both git call sites now go through a shared
helper that checks the process exit status and errors out instead of
silently reporting success on a failed checkout/update-index, with
test coverage against real temporary git repos.

src/main.rs

@@ -5,7 +5,7 @@ use env::config::{load_config, DevToolsConf};
 use crate::{
     arguments::Arguments,
     config::parse::{set_dot_env, set_local_db},
-    git::command::toggle_index,
+    git::command::{restore_connections_env, toggle_index},
 };
 use clap::Parser;
 
@@ -23,8 +23,14 @@ fn main() -> Result<()> {
 
     start_docker_compose(&config.container_service, &config.container_dir, start)?;
 
-    print!("{}", set_local_db(start, &config)?);
+    if start {
+        print!("{}", set_local_db(start, &config)?);
+    }
     toggle_index(start, &config)?;
+    if !start {
+        restore_connections_env(&config)?;
+        println!("[!] conf/global/connections.env restored to committed state.");
+    }
     print!("{}", set_dot_env(start, &config)?);
 
     println!(