docs: remove note abount autoplan modules limitation (runatlantis#5077)

Signed-off-by: akihiro17 <[email protected]>
Co-authored-by: akihiro17 <[email protected]>

Author: akihiro17

runatlantis.io/docs/server-configuration.md

@@ -185,10 +185,6 @@ Values are chosen in this order:
 By default, changes to modules will not trigger autoplanning. See the flags below.
 :::
 
-::: warning NOTE
-If any projects are defined in a repo atlantis.yaml file, the logic for this flag will not execute. See issue [#3122](https://github.com/runatlantis/atlantis/issues/3122).
-:::
-
 ### `--autoplan-modules`
 
 ```bash
@@ -202,10 +198,6 @@ Included project are projects with files included by `--autoplan-file-list`.
 After tracing, Atlantis will plan any project that includes a changed module. This is equivalent to setting
 `--autoplan-modules-from-projects` to the value of `--autoplan-file-list`. See below.
 
-::: warning NOTE
-If any projects are defined in a repo atlantis.yaml file, the logic for this flag will not execute. See issue [#3122](https://github.com/runatlantis/atlantis/issues/3122).
-:::
-
 ### `--autoplan-modules-from-projects`
 
 ```bash