How can I review this without an analysis of what you found when you worked on it!

From my notes and further thinking I created the following issues. By no means does this list claim to be complete...

Story PIPE2D-58
fit residuals from model for wavelength calibration

Story PIPE2D-57
Name calibration files according to the data model

Story PIPE2D-52
Set mask values during spectrum extraction

Story PIPE2D-51
Calculate covariance matrix during spectrum extraction

Story PIPE2D-50
reconstruct a SpectrumSet from a pfsArm file

Story PIPE2D-49
Add doxygen markup to all classes/functions

Story PIPE2D-48
Change extraction tasks to read FiberTrace parameters from disk

Story PIPE2D-47
make FiberTrace persistable

Story PIPE2D-46
write task to extract and wavelength-calibrate non-Arcs

Story PIPE2D-45
Explain structures in assembled CCD images

Story PIPE2D-44
Find out why amplifiers in assembled CCD are still distinguishable

Story PIPE2D-43
clean pfsMapper.py of copied functions or make it inherit from HSC mapper

Story PIPE2D-42
remove "super" from python classes

Epic PIPE2D-41
Fill place holders in pfsArm data model

Bug PIPE2D-40
Add config parameter 'doPlot' to drp_stella reduceArc(RefSpec)Task.py

Bug PIPE2D-38
Fix raw input name interpretation according to data model

Bug INFRA-42
Add SConscript file to bin.src

Story PIPE2D-36
make PFS pipeline installable with eups distrib install

Story PIPE2D-34
Add config parameters for minLength and maxLength to FindAndTraceAperturesTask

Bug PIPE2D-33
Sort out Spectrum containers

Added list of issues I filed while working on this ticket

Looks good. I've added a number of comments to these tickets.

Could you respond to my query on PIPE2D-51 by updating the description?

The summary for PIPE2D-57doesn't really capture the scope of the work described in the description. Please remember that people other than you will read the summaries without your detailed knowledge of the issue. This may not be worth changing in this case. In general, the descriptions in the new tickets are a little short. I can't always understand exactly what needs to be done – a short paragraph or two, rather than a single sentence would help.