MASSIVE update in preparation for Version PUDL 3.0

Besides what is listed below, there have been:

• Countless additions to method comments.
• File reorganization.
• Code formatting cleanup.

PUDL:

• Added specific types of Exceptions that all inherit from pudlException.
• Timeouts are now supported by most database drivers.
• Removed all references to global $db variable.
• pudl::$version (variable) replaced by pudl::version (constant).
• Added several more ::version_ constants.
• chunk() method no longer runs if we're not actively inside of a transaction.
• Removed support for PUDL_INDEX, PUDL_NUMBER, PUDL_BOTH. All methods will now always use PUDL_ARRAY.
• Added insertInto() and replaceInto() methods.
• Fixed JSON support in more cases.
• Added file ownership verification check. This is only used with Altaform for the time being.
• Removed MariaDB dynamic column support. We now only support JSON, since it is more universal.
• Added some UTF-8 validation testing.
• Added support for the newer Microsoft "sqlsrv" SQL Server driver.
• Legacy drivers (MySQL, MSSQL) must now be specified with "-deprecated"
• Database instance type names are now fully case insensitive.
• Added several aliases for database instance type names, such as "mariadb" and "percona"
• Added better security to session cookies in pudlSession.
• Removed HTML from error messages.
• The "prefix" configuration option now takes in an array to handle multiple prefix replacements and automatic prefix adding.
• Removed all references to $die, instead Exceptions are thrown that can be caught in cases where we don't want execution to end.
• Persistent connections are now optional everywhere.
• Changed all references from _clause() to _where() internally.
• All references to external libraries getvar and afUrl have been removed.
• Added class type hints in several locations.
• Removed $pudl->query('SQL QUERY') support, should now only use invoke via $pudl('SQL QUERY').

Query Generator:

• GENERATED columns are better detected now.
• Added method addVersioning($table) to add versioning support to a database table.
• Added experimental new syntax for simplified JOINs.
• Removed support for "LOCK FOR UPDATE" in normal method calls.
• Added support for "LOCK FOR UPDATE" to selex method.
• "UPSERT" now supported in most database engines.
• Selex now supports "HAVING" and "ON".
• Added experimental CTE support.

File Importer:

• Now throws exception instead of silently ignoring errors.
• Errors now report full JSON data, rather than just row number, to help debug data errors.

Unit Tests:

• PUDL object is now passed into every single test, so we can use multiple instances.

MySQL:

• Added check for read-only mode.

Galera:

• Added support for error code 1927 "CONNECTION WAS KILLED"
• Added randomization to connection retry, to help ensure we're not hammering a new server with many connections all at once.

Sqlite, PDO, PostgreSQL, SqlSrv:

• All massively updated to be closer to MySQL variant drivers.

pudlObject:

• Added several more methods: ** exclude() ** search() ** random() ** map() ** values() ** trim() ** ltrim() ** rtrim() ** sum() ** min() ** max() ** chunk()