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All of Lightify’s settings live in a single WordPress option, lightify_settings, stored as an associative array.
Toggles are the strings on and off, not booleans. A key that has never been seeded is absent from the array, and absent counts as off.
Prefer the settings screen or the PUT /settings endpoint over writing the option directly. Both merge your values over the stored ones and fire the update hooks; a direct update_option with a partial array silently discards every setting you left out.
To change one value safely in code:
Changing a setting does not rebuild cached pages. Purge afterwards, or visitors keep receiving pages built under the old configuration.

When keys are seeded

Free defaults are written on activation. Pro defaults are added when a licensed install first loads, and again after an update for any key that did not exist before. Your existing values are never overwritten. Several Pro keys default to on, so activating a license enables those optimizations immediately. Purge after activating.

Free settings

Pro settings

These keys only exist on an install with an active license.

Exclusion list format

pageCacheExclusions, deferJsExclusions, delayJsExclusions, and removeUnusedCssInclusions are all newline-separated strings, not arrays.
Each has a matching filter that is usually the better choice in code, since it keeps the list in version control rather than in the database. See asset optimizations.