Fixes #1201: Make list indentation and spacing consistent for all items.

This commit takes the suggestions in issue number #1201 and applies them
to the entire list. Specifically, this commit does the following:

- Replaces asterisks (`*`) with single dashes (`-`) for list items.
- Indents sub-lists (e.g., dependencies) by two spaces.
- Uses the same number of dashes for creating horizontal rules.
- Removes extra lines to make space around each heading consistent.

Additionally, this commit moves and indents `ympd` to correctly reflect
its parent dependency (`mpd`), alphabetizes the `Phproject` line item as
per the list suggestions (items should be alphabetized in their
respective categorical sub-list), and renames the "Custom" heading to
provide better clarity ("Custom communication systems"), setting the
links to that heading item to its new name.