Only consider primary flows in the topological sort

[tsmbland]

Description

Since non-primary outputs are not considered in the investment algorithm (i.e. agents only consider processes for which the demanded commodity is the primary output), we don't need to include non-primary flows in the topological sort. This may help a little bit with the circularities problem because some flow cycles may disappear (or shrink) if you only consider primary flows. See the discussion in #914

Another benefit of this PR is that we can annotate the outputted DOT graphs to highlight primary vs non-primary flows. Here I've made it so non-primary flows appear as dashed lines.

[codecov]

Codecov Report

❌ Patch coverage is 92.00000% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 84.96%. Comparing base (a942fd0) to head (0a12365).
⚠️ Report is 16 commits behind head on main.

Files with missing lines	Patch %	Lines
src/graph.rs	92.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #949      +/-   ##
==========================================
+ Coverage   84.88%   84.96%   +0.07%     
==========================================
  Files          50       50              
  Lines        5364     5419      +55     
  Branches     5364     5419      +55     
==========================================
+ Hits         4553     4604      +51     
- Misses        579      581       +2     
- Partials      232      234       +2     

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[dalonsoa]

This looks really good, and I think it makes sense thinking on circularities.

[alexdewar]

Makes sense to me!