Disable adding unstaged files when aider --commit is called from CLI

Currently, running `aider --commit` will add all unstaged files and then
create a commit. However, a useful workflow using aider may involve just
staging a few files and then calling `aider --commit` to commit those
files.

In fact, I believe this to be the sensible default. Therefore, this PR
passes the information whether the commit was triggered explicitly from
the command line interface (CLI), or rather internally later. If it was
triggered from CLI, then after this change aider will not append the
`-a` flag to the `git commit` command.

aider/commands.py

@@ -239,14 +239,14 @@ def run(self, inp):
     # any method called cmd_xxx becomes a command automatically.
     # each one must take an args param.
 
-    def cmd_commit(self, args=None):
+    def cmd_commit(self, args=None, from_cli=False):
         "Commit edits to the repo made outside the chat (commit message optional)"
         try:
-            self.raw_cmd_commit(args)
+            self.raw_cmd_commit(args, from_cli=from_cli)
         except ANY_GIT_ERROR as err:
             self.io.tool_error(f"Unable to complete commit: {err}")
 
-    def raw_cmd_commit(self, args=None):
+    def raw_cmd_commit(self, args=None, from_cli=False):
         if not self.coder.repo:
             self.io.tool_error("No git repository found.")
             return
@@ -256,7 +256,7 @@ def raw_cmd_commit(self, args=None):
             return
 
         commit_message = args.strip() if args else None
-        self.coder.repo.commit(message=commit_message)
+        self.coder.repo.commit(message=commit_message, add_unstaged=(not from_cli))
 
     def cmd_lint(self, args="", fnames=None):
         "Lint and fix in-chat files or all dirty files if none in chat"

aider/main.py

@@ -663,7 +663,7 @@ def get_io(pretty):
         if args.dry_run:
             io.tool_output("Dry run enabled, skipping commit.")
         else:
-            coder.commands.cmd_commit()
+            coder.commands.cmd_commit(from_cli=True)
 
     if args.lint or args.test or args.commit:
         return

aider/repo.py

@@ -96,7 +96,7 @@ def __init__(
         if aider_ignore_file:
             self.aider_ignore_file = Path(aider_ignore_file)
 
-    def commit(self, fnames=None, context=None, message=None, aider_edits=False):
+    def commit(self, fnames=None, context=None, message=None, aider_edits=False, add_unstaged=True):
         if not fnames and not self.repo.is_dirty():
             return
 
@@ -130,7 +130,7 @@ def commit(self, fnames=None, context=None, message=None, aider_edits=False):
                 except ANY_GIT_ERROR as err:
                     self.io.tool_error(f"Unable to add {fname}: {err}")
             cmd += ["--"] + fnames
-        else:
+        elif add_unstaged:
             cmd += ["-a"]
 
         original_user_name = self.repo.config_reader().get_value("user", "name")