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Open Settings > External tools, set the required path, and click Check tools. Matroska files prefer mkvextract and only fall back to ffprobe when it cannot be launched. General media needs ffprobe. BDMV needs BDMV/PLAYLIST and uses the built-in parser, not eac3to.
Save uses the configured Settings > General > Default save directory, then the loaded-source directory. CLI can use --output for a one-off path. The file name is the source base name plus output extension; the status area displays the effective output directory.
Choose it with the top selector. MPLS/IFO can be merged from the context menu. In the CLI, run inspect first and explicitly select with --group-index, --entry-index, or --entry-id.
Title templates, chapter-number offset, and some output rules are output projections. They primarily affect preview and save. Use F11 to view final output, or refresh the table. Lua timestamp expressions participate in refresh while preserving original imported data for re-projection.
Choose the correct frame rate. Enable Round frames for integers, or disable it and configure decimal display in Settings > Editing. Colors compare nearest-frame error with the configured threshold. Selecting a rate changes display only; use Convert to current frame rate to alter timestamps.
Check Settings > Output defaults. GUI supports UTF-8/16/32 and byte order with optional BOM; the default is UTF-8 without BOM. CLI convert uses the same default but can override it with --encoding and --bom.
The settings file is %LOCALAPPDATA%\ChapterTool\settings.json on Windows, ~/Library/Application Support/ChapterTool/settings.json on macOS, and ~/.local/share/ChapterTool/settings.json on Linux. The folder button opens this location; daily logs are in logs/.
Click Logs or press Ctrl+L. For reports, include diagnostic codes and technical details, not only a status-bar screenshot. Run chaptertool formats to list registered importers and exporters.