fix: eliminate duplicate Configuration init and add --config CLI arg

[octo-patch]

Fixes #197

Problem

When any CLI command is executed, Configuration() is instantiated twice:

1. First instantiation — the module-level config = Configuration() in configuration.py fires as a side-effect of the import statement in cli.py.
2. Second instantiation — cli.py explicitly calls config = Configuration() before init_config().

This is unnecessary: the module-level instance is never consumed by any code path — online_query.py and offline_loading.py access configuration.default_searcher, configuration.vector_db, etc., which are set only by init_config().

Solution

1. Remove the unused config = Configuration() module-level statement from configuration.py.
2. Move config initialization in cli.py to after argument parsing (avoids any startup overhead before the user's intent is known).
3. Add a --config flag to the CLI so users can specify a custom YAML path without editing source files, as suggested in the issue thread.

Testing

• Verified Configuration.__init__ is called exactly once when running a CLI command after the patch.
• Existing examples and main.py are unaffected — they always instantiated Configuration() themselves and passed it to init_config().

[sre-ci-robot]

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[octo-patch]

/assign @xiaofan-luan