Use cursor keys, drag or cut-and-paste?
If you are manually rearranging nodes within a small range of the tree you may prefer to use the cursor keys over the mouse, since using the keyboard requires less attention and coordination. However, unlike navigating using the cursor keys, you cannot currently move a node beyond the top or bottom of its current subtree without changing from the Up⁄Down keys to the Left⁄Right keys. E.g., to move a node to the next subtree up, you have to move it left using Shift+Left to the next level up in the tree hierarchy, then Shift+Up to the next subtree, then Shift+Right to make it a child of that subtree, then Up if necessary to position it in that subtree.
Cutting a node from its present position and pasting it elsewhere in the tree is an attractive alternative to having to drag it, and is the method of choice for transferring a node or subtree from one end to another of a long tree within a file that does not contain hyperlinks, or between two files of this type. This is covered in detail in Cutting⁄Copying⁄Pasting nodes and subtrees.
Once you start using hyperlinks you should be aware that cutting and reinserting a subtree reorders the IDs of all the nodes within it1, so that all hyperlinks pointing to these nodes (both internal and external to the moved subtree) need to be individually re-linked afterwards. This can be quite a time-consuming task, not to mention the possibility of overlooking some hyperlinks. For this reason it is best not to cut and paste nodes containing hyperlinks them but to use the cursor keys to move them, or to drag them with the mouse. See Re-linking hyperlinks. All Bookmarks to these nodes will also be lost, since they are automatically deleted when their target node IDs are no longer valid.
See How to split a hyperlinked subtree for an application of this.

  1. What actually happens in Cut and Paste is that the node or subtree is copied to the Treepad Clipboard, but deleted from the source file tree. The remaining nodes in the source tree retain their current IDs. The node(s) in the TreePad Clipboard have new IDs assigned to them. If they are pasted back into the original file or another file, they must again be reassigned a new set of IDs different from those of existing nodes in that file, so are given the next numbers in the ID series. So, if a subtree is cut and reinserted into the original tree, the data in the articles is not affected, but the node IDs are completely new, and so hyperlinks and bookmarks pointing to the original (now deleted) nodes are invalid.
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