Fix #140, #142, #143, #144, #145, #146

[ryan-kipawa]

Closes #140, closes #142, closes #143, closes #144, closes #145, closes #146.

• Database.create(overwrite=True) deletes the existing file before validating arguments #140 create(overwrite=True) validates srid/projection_string before deleting anything.
• to_sql and by_muid(str) don't escape single quotes #144 to_sql doubles single quotes and maps bools to 1/0; by_muid(str) goes through it.
• Tool progress handlers are attached after the work runs; warnings discarded #145 Progress handlers attach before the tool runs; CathSlopeLengthProcess reports its warnings with warnings.warn.
• Alternative.scenarios raises when a non-base scenario exists, and matches across groups #142 Alternative.scenarios walks the scenario tree (GetScenarios() returns names, not IDs) and matches on group as well as AltId; Alternative.__eq__ compares the group too.
• Database.run returns normally when the simulation fails #143 run() raises RuntimeError if the engine's ExitCode is non-zero or a result file is missing, naming the *.log / *ErrorLog.html files written during the run.
• Smaller scenario/tool API inconsistencies #146
  • Iterating db.scenarios walks the tree from BaseScenario, so duplicate-named scenarios are distinct; find_by_name returns all matches.
  • AlternativeGroup.__iter__ walks the whole tree.
  • TopoRepairTool.run raises ValueError on unsupported models.
  • close() always returns None.
  • Removed the always-false InvalidFileException check (imported from plistlib).
  • ImportTool(config, database=None) and the .mupp reading were already fixed on main.

Keeps the Harper proofread in docs-check and docs CI, with the .NET and MIKE+ identifiers it flagged added to docs/dictionary.txt. Harper reads the dictionary in order, so an uppercase entry must come before its lowercase twin. A few real prose findings are fixed too.

Fixes the pre-existing ruff import-sort failure in mikeplus/tools/__init__.py.

Tested locally against MIKE+ 2026: utils, queries, database, scenarios, tools and simulation tests, including slow ones (116 passed). Each fix has a new test.

🤖 Generated with Claude Code

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