Compare

C in the tree, with the screen split, compares the files of the current directory with those of the other window’s directory and tags, as you choose:

• Unique: not present on the other side;
• Newer and Older;
• Identical: same size and date;
• Different;
• All new: unique + newer, what is missing to bring the other side up to date.

B (or Alt+C in the tree, as in ZTreeWin) switches the scope to the whole branch: Xylem logs the branch, compares following the relative paths (src/a.rs ↔ <other>/src/a.rs) and opens the Branch with the tagged files.

Dates up to 2 seconds apart count as equal (FAT and exFAT keep times in steps of 2 seconds); compare_ignore_1h also ignores differences of exactly one hour (daylight saving time). Both are on page 4 of the configuration.

To synchronize: C B A and then Alt+C (copy with paths), which already suggests the other window as the destination.