docs: simplify default tool configurations and update documentation

Author: mrT23

docs/docs/usage-guide/automations_and_usage.md

@@ -101,37 +101,41 @@ When this parameter is set to `true`, Qodo Merge will not run any automatic tool
 
 #### GitHub app automatic tools when a new PR is opened
 
-The [github_app](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L108) section defines GitHub app specific configurations.
+The [github_app](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L220) 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.
+The configuration parameter `pr_commands` defines the list of tools that will be **run automatically** when a new PR is opened:
 ```toml
 [github_app]
 pr_commands = [
     "/describe",
     "/review",
-    "/improve --pr_code_suggestions.suggestions_score_threshold=5",
+    "/improve",
 ]
 ```
 
 This means that when a new PR is opened/reopened or marked as ready for review, Qodo Merge will run the `describe`, `review` and `improve` tools.  
-For the `improve` tool, for example, the `suggestions_score_threshold` parameter will be set to 5 (suggestions below a score of 5 won't be presented)
 
 You can override the default tool parameters by using one the three options for a [configuration file](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/): **wiki**, **local**, or **global**.
-For example, if your local `.pr_agent.toml` file contains:
+For example, if your configuration file contains:
+
 ```toml
 [pr_description]
 generate_ai_title = true
 ```
-Every time you run the `describe` tool, including automatic runs, the PR title will be generated by the AI.
 
-To change which tools will run automatically when a new PR is opened, you can set the `pr_commands` parameter in the configuration file.
+Every time you run the `describe` tool (including automatic runs) the PR title will be generated by the AI.
+
+You can customize configurations specifically for automated runs by using the `--config_path=<value>` parameter.
+For instance, to modify the `review` tool settings only for newly opened PRs, use:
 ```toml
 [github_app]
-pr_commands = ["describe", "review"]
+pr_commands = [
+    "/describe",
+    "/review --pr_reviewer.extra_instructions='focus on the file: ...'",
+    "/improve",
+]
 ```
 
-In this case, only the `describe` and `review` tools will run automatically when a new PR is opened.
-
 #### GitHub app automatic tools for push actions (commits to an open PR)
 
 In addition to running automatic tools when a PR is opened, the GitHub app can also respond to new code that is pushed to an open PR.

pr_agent/settings/configuration.toml

@@ -219,7 +219,7 @@ override_deployment_type = true
 handle_pr_actions = ['opened', 'reopened', 'ready_for_review']
 pr_commands = [
     "/describe --pr_description.final_update_message=false",
-    "/review --pr_reviewer.num_code_suggestions=0",
+    "/review",
     "/improve",
 ]
 # settings for "pull_request" event with "synchronize" action - used to detect and handle push triggers for new commits
@@ -231,27 +231,27 @@ push_trigger_pending_tasks_backlog = true
 push_trigger_pending_tasks_ttl = 300
 push_commands = [
     "/describe",
-    "/review --pr_reviewer.num_code_suggestions=0",
+    "/review",
 ]
 
 [gitlab]
 url = "https://gitlab.com"
 pr_commands = [
     "/describe --pr_description.final_update_message=false",
-    "/review --pr_reviewer.num_code_suggestions=0",
+    "/review",
     "/improve",
 ]
 handle_push_trigger = false
 push_commands = [
     "/describe",
-    "/review --pr_reviewer.num_code_suggestions=0",
+    "/review",
 ]
 
 [bitbucket_app]
 pr_commands = [
     "/describe --pr_description.final_update_message=false",
-    "/review --pr_reviewer.num_code_suggestions=0",
-    "/improve --pr_code_suggestions.commitable_code_suggestions=true --pr_code_suggestions.suggestions_score_threshold=7",
+    "/review",
+    "/improve --pr_code_suggestions.commitable_code_suggestions=true",
 ]
 avoid_full_files = false
 
@@ -276,8 +276,8 @@ avoid_full_files = false
 url = ""
 pr_commands = [
     "/describe --pr_description.final_update_message=false",
-    "/review --pr_reviewer.num_code_suggestions=0",
-    "/improve --pr_code_suggestions.commitable_code_suggestions=true --pr_code_suggestions.suggestions_score_threshold=7",
+    "/review",
+    "/improve --pr_code_suggestions.commitable_code_suggestions=true",
 ]
 
 [litellm]