docs: fix formatting and links in troubleshooting
Converted plain text references to Markdown links across the troubleshooting documentation and index.md. Converted commands to properly formatted inline code blocks, and ensured code blocks conform to the SSOT's indented-block requirements.
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@@ -35,7 +35,7 @@ output, file contents, and secrets printed to the terminal. Nothing leaves
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your machine, but the files persist locally.
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- Disable all logging with: `set -U __fish_config_op_logging off`
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- Prefer a menu? Run the interactive picker: `config-settings`
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- See Section 7 (C5 - Logging and Capture) for the full breakdown.
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- See [C5 — Logging and Capture](/07-customization/#c5--logging-and-capture) for the full breakdown.
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The configuration uses a structured file tree:
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