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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. 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. 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 💎 1. [Wiki](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/#wiki-configuration-file)configuration page 💎
2. Local configuration file 2. [Local](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/#local-configuration-file) configuration file
3. Global 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. In terms of precedence, wiki configurations will override local configurations, and local configurations will override global configurations.