How to modify a file inside a pod through helm if that directory is not in helm chart?

There isn't. Helm only runs a templating layer to create Kubernetes API objects and submit them to the cluster, and nothing at the Kubernetes API layer is able to manage individual files. There are limited exceptions like being able to mount a ConfigMap into a Pod, but this is standard Kubernetes functionality and nothing Helm-specific.

You usually shouldn't try to make manual changes inside a running pod. These won't persist if the pod is deleted, something that happens extremely routinely (if you update a Deployment with a new image:; in response to a HorizontalPodAutoscaler; if the node it's on fails). A better approach is to make whatever changes you need to make in your image's original Dockerfile, or to set up the image to configure itself correctly as part of the startup sequence.