Commit 455d780c did add the:

  extensions = ["sphinx.ext.autosectionlabel"]

which provoques 2 problems:
- previous extensions (from swh.doc) are disabled,
- this autosectionlabel extension does produces a lot of "duplicate label"
  warnings.

So get rid of this line in conf.py and use explicit labels in
spec-meta-deposit.rst.

Also fix an indentation problem in this file.