Handle nested tables in TOML encoder

[roxblnfk]

What was changed

• Fixed TOML encoder losing nested tables during encoding
• Added flattenData() method to convert nested structures to dotted keys
• Added fixture-based round-trip test for complex TOML files

Why?

Encoder was silently dropping nested table data (e.g., github.token,
github.plugins.*). This broke round-trip encoding/decoding for real-world TOML
configs.

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