The file currently being edited can be saved at any time using the ribbon Save 
button.
You can also use the commands in the Save 
and Save as… 
submenus of the Application menu 
(Merge 2020 and later) or File menu (Merge 2019 or earlier). Use Save to save modifications back to a file. Use Save as… to save a file with a new name. Equivalent commands are also available from the context menu that is displayed when you right-click a file panel.
Choosing the line ending type
If you select Save as… 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 as… dialog contains a list of all the character encodings that are supported by your computer. By default, files are saved using the system-wide default encoding configured in the Windows control panel.
Please see the Working with Character Encodings topic for more information about character encodings, code page, and language support in Merge.
Saving compressed files
You can save a file compressed with the gzip or bzip2 formats by specifying .gz or .bz2 as the file extension. (This assumes that the default file types for these extensions are enabled on the File Types options page.)