The file currently being edited can be saved at any time by using the Save 
toolbar button.
You can also use the File▸Save menu items to save modifications back to a file, and the File▸Save As menu items to save a file with a new name. These menu items are also available from the context menu that is displayed when you right-click a file panel.
Choosing the line ending type
If you use File▸Save As menu item to save a file, you can choose whether to save the file with Windows-style (CR LF), UNIX-style (LF) or Macintosh-style (CR) line endings. Alternatively, you can choose to preserve the existing line endings.
If you elect to preserve existing line endings, you should be aware that Merge applies the predominant (that is, the most common) line endings of an existing file to new text when it is inserted into the file. This is true whatever the mechanism used to insert the text (merging from one file to another, editing, pasting from the clipboard, drag and drop).
Choosing a character encoding
You can also choose the character encoding that is used to save the file. A drop-down list in the Save File As sheet contains a list of all the character encodings that are supported by your computer.
Please see the Working with Character Encodings topic for more information about the character encoding support in Merge.