There is one box: Ttop, the manual's root type. Every keyword valid at the top level of an INP file is somewhere beneath it. By-topic chapters (indexing, charge-flipping, ...) aren't separate boxes -- their keywords are folded into Ttop's tree wherever the manual references them (e.g. TIndexing, TCharge_flipping).
A line can have nested detail and/or reference another Txxx complex type (blue -- meaning "everything defined under that type's heading also belongs here", not a nested sub-object). The same type is reused under several parents at once, so a shown ancestry -- or a Get result -- may not be the only valid path.
Opening and closing. −/+ on a line collapse and expand it one level at a time, and hide themselves once there is nothing left to do. The triangle at the start of a line opens that one line all the way. On Ttop's own row, ↑/↓ collapse and expand the whole tree. Clicking a name never opens or closes anything -- neither a keyword, nor a Txxx type, nor Ttop itself; names only drive the panels on the right.
Click a keyword to set it as the Get search root and show its description. Get(xx) searches up from that root through ancestors (checking each ancestor's name first, then its nested detail), passing straight through any complex type crossed along the way. Get(xx, yy, ...) chains: equivalent to clicking xx then typing Get(yy). A trailing ... means more than one can occur, so a Child(xx) result only lands on the first -- a warning names the ambiguity when that happens.
In Parents/Inherited by, clicking a keyword's name scrolls to and highlights it in the tree; clicking a Txxx type name in either panel instead shows that type's own tree in the secondary view, leaving both panels untouched.
Clicking a keyword also fills Inherited by with every other place its nearest complex-type ancestor is used. Clicking a complex type does the same directly.
Filter doesn't search as you type -- press Enter. Comma-separate several terms. A term matches whole words first; substring matching only kicks in when no exact match exists anywhere. Case: ON/OFF sets case-sensitive vs. -insensitive matching (defaults ON, matching TOPAS's case-sensitive syntax).
The manual. A star on a line opens the Technical Reference in the secondary view, at that keyword. The star on Ttop's own row opens it at the beginning, which is also what the secondary view shows the first time you enter the tree. The whole manual is embedded in this page -- nothing is fetched, and it works offline. The first star click has to load it and takes a moment; every later one is instant. Use the browser's own find (Ctrl+F) to search inside it.
Collapsing the manual works like Word's outline view. Click anywhere in the document to put the cursor in a section -- its heading is highlighted. − in the panel header then collapses that section; pressing it again, on a title already collapsed, collapses the section above it, so repeated presses fold outwards. + expands the focused section by one level, and is only available once a section title has been clicked. Every heading also carries its own −/+. Clicking a star clears all collapsing, so a keyword jump always lands in a readable document; following a cross-reference inside the manual opens only what it needs to.
Contents (the ☰ button) lists every chapter and section, with −/+ at its header to close or open all chapters at once. Drag its left edge to widen or narrow it; it starts at its usual width each time the document loads.
Searching the manual. The box at the top of Contents searches the whole document -- type and press Enter, and the chapter list is replaced by every match, grouped under the section it falls in, with a count per section. Aa toggles case sensitivity. Clicking a result jumps to that occurrence, expanding its section first if it was collapsed; every match is highlighted in the document at once. Hits in the manual's own table of contents are listed last, so they can't bury the real ones. Clear the box (or press Esc) to get the chapters back. The browser's own Ctrl+F still works and is quicker for a single jump -- this is for seeing where a term occurs across the whole manual.
Moving around. The browser's own Back and Forward buttons move between this page, the tree, and the Introduction -- there is no in-page back button. Help on Ttop's row returns here. Inside the manual, the ◀/▶ triangles in the panel header step back and forward through the last 20 places you jumped to -- stars, cross-references, Contents entries and search results all count. They are greyed when there is nowhere to step.