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docs: improve configuration options documentation with better formatting and links

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docs/docs/usage-guide/configuration_options.md
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The different tools and sub-tools used by Qodo Merge are adjustable via the **[configuration file](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml)**.
The different tools and sub-tools used by Qodo Merge are adjustable via a configuration file.
In addition to general configuration options, each tool has its own configurations. For example, the `review` tool will use parameters from the [pr_reviewer](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L16) section in the configuration file.
See the [Tools Guide](https://qodo-merge-docs.qodo.ai/tools/) for a detailed description of the different tools and their configurations.
There are three ways to set persistent configurations:
There are three main ways to set persistent configurations:
1. Wiki configuration page 💎
2. Local configuration file
3. Global configuration file 💎
1. [Wiki](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/#wiki-configuration-file)configuration page 💎
2. [Local](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/#local-configuration-file) configuration file
3. [Global](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/#global-configuration-file) configuration file 💎
In terms of precedence, wiki configurations will override local configurations, and local configurations will override global configurations.