An actual tree in the dungeon and a metaphor for existence itself — its fruit fed the old gods and impregnated Apito.
The All-Tree is, per Rosetta's myth-lecture, both a literal tree that exists within the dungeon and a metaphor for existence itself. In the origin story, the tree gave its fruit to the old, wilder gods who preceded the current pantheon — including the vulture goddess Nekhebit — and it is by the All-Tree (or by making herself pregnant, the myth varies) that Nekhebit's daughter Apito conceived the children who would overthrow the old order. From the prior books, the reader knows the tree is a real place in the dungeon's cosmology, into which the sacrificed Li Jun was taken.
As the loose gods, Sheol, the Cabaret, and the Scavenger's Daughter myth all converge on the endgame, the All-Tree stands as the mythic root of the whole divine order the crawlers are now tangled in.
Described as an actual tree within the dungeon and, simultaneously, a metaphor for all existence.
The mythic world-tree at the root of the dungeon's pantheon — literal tree and metaphor for existence.
Also appears in books you've already read — spoiler-safe to their endings: