The Professional Edition of Merge has the ability to automatically merge two modified files into a common ancestor. A typical merging scenario is where two developers have independently made modifications to a source file stored in a configuration management system and changes in the two modified files need to be reviewed and merged together.
Starting an automatic merge
Automatic merging works only with three-way file comparisons. The common ancestor file should be loaded into the central file panel and the two newer (modified) files into the left and right panels. You should ensure that the common ancestor folder is the one in the centre of the folder comparison window if you are using a three-way folder comparison window to launch file comparison windows.
Use the 
button to start an automatic merge.
How automatic merging works
When an automatic merge is started, Merge will examine the three files starting at the top, working down. Each change between the three files is examined to determine whether it should be retained in, or added to, the final merged file. Merge may be unable to decide what to do with certain types of change and will mark them as conflicts that require attention from you.
When the merge is complete, the central file panel will contain the resolved (merged) file. This is therefore the file that you should save once you are happy with the merge results. The left and right-hand files are not modified by the three-way merge command.
Simple rules control how changes in the two modified files are merged into the common ancestor. Since the two modified files are assumed to be more recent than the common ancestor, changes (inserted, removed, or edited blocks of lines) to the files are applied into the common ancestor unless changes to the two modified files overlap.
Understanding automatic merge results
Changes that overlap or touch at their start or end are marked as conflicts. A red conflict icon 
is shown at the beginning of each line within a change that could not be automatically merged. You can navigate between conflicts
by using the 
and 
buttons in the toolbar or the commands in the Markers section of the Edit
menu.
There are some types of overlapping change that do not result in a conflict. If the change is the same in the modified files (for example, the same lines were added/removed/changed, and their content is exactly the same) then the change is merged into the common ancestor. Merge always treats whitespace as significant when deciding whether to automatically merge a particular change. Thus, if a change appears identical in the modified files but Merge has marked it as a conflict, it is likely that there is a difference in whitespace or line endings between the two modified files.
Marking of changes made to the common ancestor file
Every change that is made to the common ancestor is flagged with an edit marker 
. If lines are introduced into the common ancestor, then a small arrow next to the edit marker 
indicates the file from which the lines were copied. If lines are removed from the common ancestor, then a delete marker
is placed on the line after the position at which the lines were removed.
Each edit marker has an associated tool tip that explains why the edit was made. Hold the mouse cursor over the marker for a few seconds to see the tool tip. Conflict markers also have tool tips to explain the reason for the conflict.
You can navigate between edit markers using the Previous/Next Edit 
buttons in the toolbar or Markers section of the Edit menu.
Dimming of resolved lines
As Merge resolves the changes between the two modified files into the common ancestor, the resolved lines are dimmed to indicate that they have been finished with. When the three-way merge is complete, only lines within conflicting changes will retain their original colours. The amount of dimming applied to resolved lines is controlled by the Dimming option on the Fonts and Colours Options page.
Resolving conflicts
After performing an automatic merge, you should manually resolve any conflicting changes that were flagged. You should also check that the changes that have been made automatically to the common ancestor are valid. Finally, you may need to adjust the indentation of some of the merged changes.
Previewing an automatic merge
Because automatic merging can be undone, it is safe to try an automatic merge to see what it will do. If you are unhappy with
the automatic merge results, use the Undo 
command in the Edit menu to reverse the automatic merge.
Previewing an automatic merge is a useful way of quickly highlighting the conflicting sections of the files being compared.
Clearing markers and text dimming
Following a three-way merge operation, you can remove all of the edit/conflict markers and text dimming by using the Clear All Markers 
button in the toolbar or Markers section of the Edit menu. This will also clear any bookmarks you may have set.
At any time you can mark the current selection or line as resolved by using the Mark Resolved 
button in the toolbar or Edit menu. This will remove any conflict markers on lines within the selection and cause it to be dimmed. If there is no selection,
the operation is applied to the current line.