Write settings.json atomically

[sjoelund]

SetFlag does a read-modify-write of $HOME/.omsimulator/settings.json for the two flags that carry settings (--tempDir and --workingDir). SaveSettings opened a std::ofstream directly on that path, which truncates it. Every OMSimulator process on the machine shares the file, so a concurrent run could parse it while it was empty or half written:

warning: Failed to save settings: [json.exception.parse_error.101] parse
error at line 1, column 1: attempting to parse an empty input; check that
your input string or stream contains the expected JSON

This shows up in the OpenModelica testsuite, where 11 .mos tests pass --tempDir to OMSimulator and rtest runs them in parallel under one HOME. 40 concurrent --tempDir=... --version runs produced 23 such warnings, one of them from a reader that caught a partially written file (line 3, column 2: syntax error ... unexpected '}').

Write to settings.json.<pid>.tmp in the same directory and rename it into place instead, so a reader always sees one complete version of the file. LoadSettings now treats an empty file as "no settings" rather than throwing, which also covers a file left behind by a process killed mid-write. The same 40-way race is clean afterwards.

Assisted-by: Claude Opus 5 (1M context)

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[codecov]

Codecov Report

❌ Patch coverage is 13.51351% with 32 lines in your changes missing coverage. Please review.
✅ Project coverage is 29.24%. Comparing base (8ce1f2d) to head (6a5bf70).
⚠️ Report is 1 commits behind head on master.

Files with missing lines	Patch %	Lines
src/OMSimulatorLib/Flags.cpp	13.51%	29 Missing and 3 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1636      +/-   ##
==========================================
- Coverage   29.26%   29.24%   -0.02%     
==========================================
  Files          68       68              
  Lines       12942    12960      +18     
  Branches     8378     8389      +11     
==========================================
+ Hits         3787     3790       +3     
- Misses       7965     7979      +14     
- Partials     1190     1191       +1     

Flag	Coverage Δ
linux	29.24% <13.51%> (-0.02%)	⬇️

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