Manual: Figure and table labels are out of sync with labeling

**Describe the bug**
As noted in https://github.com/QMCPACK/qmcpack/pull/3226 , some of the captions in the manual use fixed numbering that is now incorrect. In addition, some of the labels use fixed numbers that are incorrect/out of sequence.

**To Reproduce**
Current manual at https://qmcpack.readthedocs.io/en/develop/

**Expected behavior**

Labels should be numerically sequenced consistently or use names.

**System:**

NA

**Additional context**

Unlike the original LaTeX, RST has limited autonumbering options, so this might require a "by hand" fix. Possibly there are extensions that can help but I have not investigated.

Start with the current manual at https://qmcpack.readthedocs.io/en/develop/ and compare its figure and table captions and labels with the source RST. Check the referenced pull request for context, then make numbering consistent or replace fixed numbers with names throughout the affected manual content.

Written by the indexing model from the issue text.