Fix stale docs links and navigation targets (#2232)

Replace stale references in model and configuration docs to point at
current files that exist in this repository.

Use .secrets_template.toml instead of the removed ai_handler.py path
for model-provider key setup guidance.

Normalize the configuration.toml GitHub link by removing a trailing
slash so the file URL remains stable.

Fix the "Chat on code suggestions" links in docs index and summary
to point to core-abilities/interactivity.md.

Author: PeterDaveHello

docs/docs/index.md

@@ -40,7 +40,7 @@ PR-Agent offers comprehensive pull request functionalities integrated with vario
 |       | [Actions](./installation/github.md#run-as-a-github-action)                            |   ✅   |   ✅   |    ✅     |      ✅       |       |
 |       |                                                                                       |        |        |           |              |       |
 | [CORE](./core-abilities/index.md) | [Adaptive and token-aware file patch fitting](./core-abilities/compression_strategy.md) |   ✅   |   ✅   |    ✅     |      ✅       |       |
-|       | [Chat on code suggestions](./core-abilities/chat_on_code_suggestions.md)              |   ✅   |  ✅   |           |              |       |
+|       | [Chat on code suggestions](./core-abilities/interactivity.md)                         |   ✅   |  ✅   |           |              |       |
 |       | [Compression strategy](./core-abilities/compression_strategy.md)                      |   ✅   |   ✅   |    ✅     |      ✅       |       |
 |       | [Dynamic context](./core-abilities/dynamic_context.md)                                |   ✅   |   ✅   |    ✅     |      ✅       |       |
 |       | [Fetching ticket context](./core-abilities/fetching_ticket_context.md)                |   ✅   |  ✅   |    ✅     |              |       |

docs/docs/summary.md

@@ -36,7 +36,7 @@
 ## Core Abilities
 
 * [Core Abilities](core-abilities/index.md)
-* [Chat on code suggestions](core-abilities/chat_on_code_suggestions.md)
+* [Chat on code suggestions](core-abilities/interactivity.md)
 * [Compression strategy](core-abilities/compression_strategy.md)
 * [Dynamic context](core-abilities/dynamic_context.md)
 * [Fetching ticket context](core-abilities/fetching_ticket_context.md)

docs/docs/tools/help_docs.md

@@ -100,7 +100,7 @@ When a new issue is opened, you should see a comment from `github-actions` bot w
 
 ## Configuration options
 
-Under the section `pr_help_docs`, the [configuration file](https://github.com/qodo-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L50) contains options to customize the 'help docs' tool:
+Under the section `pr_help_docs`, the [configuration file](https://github.com/qodo-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L199) contains options to customize the 'help docs' tool:
 
 - `repo_url`: If not overwritten, will use the repo from where the context came from (issue or PR), otherwise - use the given repo as context.
 - `repo_default_branch`: The branch to use in case repo_url overwritten, otherwise - has no effect.

docs/docs/tools/review.md

@@ -159,8 +159,8 @@ extra_instructions = "..."
 
     The `review` can tool automatically add labels to your Pull Requests:
 
-    - **`possible security issue`**: This label is applied if the tool detects a potential [security vulnerability](https://github.com/qodo-ai/pr-agent/blob/main/pr_agent/settings/pr_reviewer_prompts.toml#L103) in the PR's code. This feedback is controlled by the 'enable_review_labels_security' flag (default is true).
-    - **`review effort [x/5]`**: This label estimates the [effort](https://github.com/qodo-ai/pr-agent/blob/main/pr_agent/settings/pr_reviewer_prompts.toml#L90) required to review the PR on a relative scale of 1 to 5, where 'x' represents the assessed effort. This feedback is controlled by the 'enable_review_labels_effort' flag (default is true).
+    - **`possible security issue`**: This label is applied if the tool detects a potential [security vulnerability](https://github.com/qodo-ai/pr-agent/blob/main/pr_agent/settings/pr_reviewer_prompts.toml#L121) in the PR's code. This feedback is controlled by the 'enable_review_labels_security' flag (default is true).
+    - **`review effort [x/5]`**: This label estimates the [effort](https://github.com/qodo-ai/pr-agent/blob/main/pr_agent/settings/pr_reviewer_prompts.toml#L105) required to review the PR on a relative scale of 1 to 5, where 'x' represents the assessed effort. This feedback is controlled by the 'enable_review_labels_effort' flag (default is true).
     - **`ticket compliance`**: Adds a label indicating code compliance level ("Fully compliant" | "PR Code Verified" | "Partially compliant" | "Not compliant") to any GitHub/Jira/Linea ticket linked in the PR. Controlled by the 'require_ticket_labels' flag (default: false). If 'require_no_ticket_labels' is also enabled, PRs without ticket links will receive a "No ticket found" label.
 
 

docs/docs/tools/similar_issues.md

@@ -68,4 +68,4 @@ You can get a free managed Qdrant instance from [Qdrant Cloud](https://cloud.qdr
 - To invoke the 'similar' issue tool via online usage, [comment](https://github.com/qodo-ai/pr-agent/issues/178#issuecomment-1716934893) on a PR:
 `/similar_issue`
 
-- You can also enable the 'similar issue' tool to run automatically when a new issue is opened, by adding it to the [pr_commands list in the github_app section](https://github.com/qodo-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L66)
+- You can also enable the 'similar issue' tool to run automatically when a new issue is opened, by adding it to the [pr_commands list in the github_app section](https://github.com/qodo-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L229)

docs/docs/tools/update_changelog.md

@@ -15,7 +15,7 @@ It can be invoked manually by commenting on any PR:
 
 ## Configuration options
 
-Under the section `pr_update_changelog`, the [configuration file](https://github.com/qodo-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L50) contains options to customize the 'update changelog' tool:
+Under the section `pr_update_changelog`, the [configuration file](https://github.com/qodo-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L169) contains options to customize the 'update changelog' tool:
 
 - `push_changelog_changes`: whether to push the changes to CHANGELOG.md, or just publish them as a comment. Default is false (publish as comment).
 - `extra_instructions`: Optional extra instructions to the tool. For example: "Use the following structure: ..."

docs/docs/usage-guide/automations_and_usage.md

@@ -29,7 +29,7 @@ verbosity_level=2
 
 This is useful for debugging or experimenting with different tools.
 
-3. **git provider**: The [git_provider](https://github.com/qodo-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L5) field in a configuration file determines the GIT provider that will be used by PR-Agent. Currently, the following providers are supported:
+3. **git provider**: The [git_provider](https://github.com/qodo-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L12) field in a configuration file determines the GIT provider that will be used by PR-Agent. Currently, the following providers are supported:
 `github` **(default)**, `gitlab`, `bitbucket`, `azure`, `codecommit`, `local`, and `gitea`.
 
 ### CLI Health Check
@@ -96,7 +96,7 @@ When this parameter is set to `true`, PR-Agent will not run any automatic tools
 
 #### GitHub app automatic tools when a new PR is opened
 
-The [github_app](https://github.com/qodo-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L220) section defines GitHub app specific configurations.
+The [github_app](https://github.com/qodo-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L223) section defines GitHub app specific configurations.
 
 The configuration parameter `pr_commands` defines the list of tools that will be **run automatically** when a new PR is opened:
 

docs/docs/usage-guide/changing_a_model.md

@@ -2,7 +2,7 @@
 
 See [here](https://github.com/qodo-ai/pr-agent/blob/main/pr_agent/algo/__init__.py) for a list of supported models in PR-Agent.
 The default model of PR-Agent is `GPT-5` from OpenAI.
-To use a different model than the default, you need to edit in the [configuration file](https://github.com/qodo-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L2) the fields:
+To use a different model than the default, you need to edit in the [configuration file](https://github.com/qodo-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L7) the fields:
 
 ```toml
 [config]
@@ -145,7 +145,7 @@ key = ...
 
 (you can obtain a Llama2 key from [here](https://replicate.com/replicate/llama-2-70b-chat/api))
 
-Also, review the [AiHandler](https://github.com/qodo-ai/pr-agent/blob/main/pr_agent/algo/ai_handler.py) file for instructions on how to set keys for other models.
+Also, review the [.secrets_template.toml](https://github.com/qodo-ai/pr-agent/blob/main/pr_agent/settings/.secrets_template.toml) file for instructions on how to set keys for other models.
 
 ### Groq
 

docs/docs/usage-guide/configuration_options.md

@@ -8,8 +8,8 @@ There are three main ways to set persistent configurations:
 In terms of precedence, wiki configurations will override local configurations, and local configurations will override global configurations.
 
 
-For a list of all possible configurations, see the [configuration options](https://github.com/qodo-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml/) page.
-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/qodo-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L16) section in the configuration file.
+For a list of all possible configurations, see the [configuration options](https://github.com/qodo-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml) page.
+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/qodo-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L66) section in the configuration file.
 
 !!! tip "Tip1: Edit only what you need"
     Your configuration file should be minimal, and edit only the relevant values. Don't copy the entire configuration options, since it can lead to legacy problems when something changes.