A good project tree browser for Emacs?

Speedbar?

If you just want to manage related files, perhaps you would like eproject.

I haven't tried this one myself yet, but emacs-nav is a new Emacs project browser from Google that seems to have the features you value.

The different parts of cedet will do what you want I think. Speedbar has the tree structure thing, and EDE handles projects etc.

Here are my thoughts on several competing file explorer type packages. See the comments above each package below:

;; Dired itself allows one to do 'i' to insert (display in same buffer) the
;; subdirectory under point and C-u k on subdir header line to remove. However,
;; I have found that dired-subtree-toggle and dired-subtree-remove are a better solution for the removal
;; part. Plus dired-subtree let's you customize colors of subdirs to set them apart
;; visually. However, I set all depths of subdirectories custom faces to be the same as I found it distracting.
(use-package dired-subtree
  :ensure t
  :bind (:map dired-mode-map ("i" . 'dired-subtree-toggle))
  :bind (:map dired-mode-map ("I" . 'dired-subtree-remove)))


;; This works nicely. It provides the parent, '..', directory unlike nav.
(use-package project-explorer
  :ensure t
  :config
  (evil-set-initial-state 'project-explorer-mode 'emacs))

;; This can't go above the directory you started it in. It is nice, but I prefer the flexibility
;; of getting to parent directories in most cases.
(use-package dirtree
  :ensure t)

;; Google's file explorer
;; Nice, but doesn't maintain visited nodes in view, preferring instead to offer only
;; the current directory or lower in a side window. No better than ivy which is my main file explorer system.
(use-package nav
  :ensure t)

;; This is buggy on Emacs 26.1.
(use-package eproject
  :disabled t
  :ensure t)

;; speedbar is included with Emacs (since 24.x I believe). It has to use a separate frame, which is
;; inconvenient most of the time. There are better options (above).
;; (use-package speedbar)

;; Buggy; doesn't work on Emacs 26.1 (at least with my config).
(use-package sr-speedbar
  :disabled t
  :load-path "../lisp")

;; Buggy on Emacs 26.1 (at least with my config). I couldn't even get it to activate.
(use-package ecb
  :disabled t
  :ensure t)

;; Nice, but similar to ivy which I've already committed to, so not necessary.
(use-package lusty-explorer
  :disabled t
  :ensure t)

For me, ivy plus dired gets me 98% of the way. ivy, dired, and dired-subtree gets me 99% of the way. project-explorer, and to a lesser extent, nav, are just nice alternatives to ivy plus dired or ivy plus dired and dired-subtree. Hopefully this will save you some time.

I've used treemacs and it's works good, esp. with projectile.