Most example configs do not load as written: 361 hard-code bng_command to the original author's machine and 280 MSA configs have a comma in output_dir #1003

Most of the example configs under examples/ cannot be loaded as written, on any machine but the one each was written on. Measured on main (68fb0d1), with find examples -name '*.conf' giving 553 configs:

1. 361 set bng_command to a path on the original author's machine.

   • 335 use bng_command = /usr/local/anaconda3/bin/BNG2.pl.
   • 26 use bng_command = /projects/posner_lab/BioNetGen-2.3.1/BNG2.pl.

   An explicit bng_command overrides BNGPATH, so each of these stops at load with "The BioNetGen simulator (BNG2.pl) was not found at the specified location". That's right for a user's own config, since a wrong explicit path should not be silently replaced, but it makes the examples unusable as shipped. Example: examples/COVID19forecasting_aMCMC/WindyCity/m3.conf.

2. 280 (examples/Mallela2022MSAs/*) have a comma in output_dir. For example, output_dir = Akron, OH_output is refused by the parser: "output_dir should be specified in the format 'output_dir=s'". These also carry the bng_command above.

3. 4 fail for other reasons: three Degranulation configs list their data files separated by spaces on the model = line, and one has a nested Louisville model path.

With bng_command and output_dir neutralized and each config loaded from its own folder, 549 of 553 load (the independent review of #1001 ran this sweep). So items 1 and 2 account for nearly every failure.

Expected

• Remove the bng_command lines. BNGPATH, or bngsim under bngl_backend = auto, covers them.
• Give the MSA examples output_dir values without commas, and check their model = lines too, since commas there also separate data files.
• Fix the four remaining configs.
• Add a test that loads every examples/**/*.conf from its own folder (BNG2.pl may be required), so the examples cannot drift again. The fix(am): record every experiment's trajectory, normalized once; refuse what would be wrong (#990) #994 and fix(config): refuse three configurations that ran to a meaningless result (#996, #997, #999) #1001 reviews each wrote such a sweep in their probes, so it could be lifted from there.