Errors and warnings missing from RMG.log

I redirected the console output from a recent RMG run to a file called RMG-tracking.log, and then did a diff comparison against the autosaved RMG.log file. In general, the autosaved RMG.log file is more verbose (as we intended) but there is some strange behaviour and discrepancies, such as warnings and errors NOT being saved in the autosaved RMG.log file (which is bad).

Missing from the RMG.log file (which should contain everything?):

Notification that a requested primary thermo library had not been loaded and RMG is not using the thermo I thought!

RMG cannot read Primary Thermo Library: CO3 /home/rwest/RMG-Java/databases/RMG_database/thermo_libraries/CO3/Dictionary.txt

Quantum Calcs details like:

Pre-existing successful quantum result for BPCSPAPFKNWIMN-JSWHHWTPCX (InChI=1/C3H2O5/c4-1(2(5)6)3-7-8-3/h3H,(H,5,6)/f/h5H) has been found. This log file will be used. Point group: C1 Thermo for BPCSPAPFKNWIMN-JSWHHWTPCX: -114.44 91.59 27.32 32.15 36.02 39.09 43.49 46.41 50.47
HBI-based thermo for OMNGFTJAWVTWBX-JSWHHWTPCO(InChI=1/C3HO5/c4-1(2(5)6)3-7-8-3/h(H,5,6)/f/h5H): -65.44 94.2 26.55 30.79 34.11 36.69 40.33 42.67 45.81
Pre-existing successful quantum result for WZIBVWJMTTXIMN-JSWHHWTPCG (InChI=1/C3H2O5/c4-1(2(5)6)3-7-8-3/h4H,(H,5,6)/f/h5H) has been found. This log file will be used. Point group: C1 Thermo for WZIBVWJMTTXIMN-JSWHHWTPCG: -105.9 89.86 28.51 32.88 36.41 39.23 43.32 46.07 50.04
HBI-based thermo for OMNGFTJAWVTWBX-JSWHHWTPCO(InChI=1/C3HO5/c4-1(2(5)6)3-7-8-3/h(H,5,6)/f/h5H): -70.0 88.75 27.17

Missing from the console output:

The copy of the user input file:

User input: etc.

Which reaction family is being used next:

Reacting Mfmt(1) with the core: R_Addition_MultipleBond

Missing from the console output, but probably rightly so (too much information)

Discrepancies in the kinetics libraries:

System temperature 600.0K not within valid Temperature Range (298K) for node: C_methyl + O_Csrad Multiple sets of Arrhenius parameters found for: C_methyl + O_Csrad. Replacing Kinetics for C_methyl + O_Csrad: From 298K data with A=8.49E13 to 300-2500K data with A=2.41E12

Pdep networks solved:

PDepNetwork #1345 (C2H2O4) solved: 190 included and 260 nonincluded net reactions.

Frankie errors:

Frankie exceeded maximum number of iterations Frankie.exe wasn't fully successful: species 3222 had output flag 8 Saving input file as 'frankie/dat.8.3222' should you wish to debug.

Things in the original issue above that have not been addressed by commits a98c98f525ecf50deb926a6271e4d240d8941a47 and f56ee7d0fa7a6037e6edf7ffa90b3cd5dc5cb5fa: