Docs: Fix wrong and missing common configuration section descriptions

[DylanGuedes]

Describe the bug
Bug 1: path_prefix configuration from the common section is wrongly describing it as When defined, the given prefix will be present in front of the endpoint paths., when it is used to compose file paths to read/write from.
Bug 2: Both, chunks_directory and rules_directory (also from the common section) aren't documented

To Reproduce
N/A

Expected behavior
N/A

Environment:
N/A

Screenshots, Promtail config, or terminal output
N/A

[stale]

Hi! This issue has been automatically marked as stale because it has not had any
activity in the past 30 days.

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[darxriggs]

This should not be closed.