edgeAgent CURRENT manifest file not accurate

## Expected Behavior
CURRENT manifest file points to the manifest file used by runtime to know which modules are deployed.

## Current Behavior
Manifest file contains many different key words, but only few of the currently deployed modules are listed.


Actual manifest contains 9 custom modules.

## Steps to Reproduce
Provide a detailed set of steps to reproduce the bug.
1. On the device, go to edgeAgent storage folder (typically /etc/aziot/storage/edgeAgent)
2. Execute: sudo strings /etc/aziot/storage/edgeAgent/$(sudo cat /etc/aziot/storage/edgeAgent/CURRENT)
3. What i did to list only user's + runtime's modules: sudo strings /etc/aziot/storage/edgeAgent/$(sudo cat /etc/aziot/storage/edgeAgent/CURRENT) | grep -v "level\|Config\|State\|mkn" | sort | uniq

## Context (Environment)
IoT Edge with 5-10 custom modules.

### Output of `iotedge check`

Click here

```

Configuration checks (aziot-identity-service)
---------------------------------------------
√ keyd configuration is well-formed - OK
√ certd configuration is well-formed - OK
√ tpmd configuration is well-formed - OK
√ identityd configuration is well-formed - OK
√ daemon configurations up-to-date with config.toml - OK
√ identityd config toml file specifies a valid hostname - OK
√ aziot-identity-service package is up-to-date - OK
√ host time is close to reference time - OK
√ preloaded certificates are valid - OK
√ keyd is running - OK
√ certd is running - OK
√ identityd is running - OK
√ read all preloaded certificates from the Certificates Service - OK
√ read all preloaded key pairs from the Keys Service - OK
√ check all EST server URLs utilize HTTPS - OK
√ ensure all preloaded certificates match preloaded private keys with the same ID - OK

Connectivity checks (aziot-identity-service)
--------------------------------------------
‼ host can connect to and perform TLS handshake with iothub AMQP port - Warning
Could not retrieve iothub_hostname from provisioning file.
Please specify the backing IoT Hub name using --iothub-hostname switch if you have that information.
Since no hostname is provided, all hub connectivity tests will be skipped.
‼ host can connect to and perform TLS handshake with iothub HTTPS / WebSockets port - Warning
Could not retrieve iothub_hostname from provisioning file.
Please specify the backing IoT Hub name using --iothub-hostname switch if you have that information.
Since no hostname is provided, all hub connectivity tests will be skipped.
‼ host can connect to and perform TLS handshake with iothub MQTT port - Warning
Could not retrieve iothub_hostname from provisioning file.
Please specify the backing IoT Hub name using --iothub-hostname switch if you have that information.
Since no hostname is provided, all hub connectivity tests will be skipped.
√ host can connect to and perform TLS handshake with DPS endpoint - OK

Configuration checks
--------------------
√ aziot-edged configuration is well-formed - OK
√ configuration up-to-date with config.toml - OK
√ container engine is installed and functional - OK
√ configuration has correct URIs for daemon mgmt endpoint - OK
√ aziot-edge package is up-to-date - OK
√ container time is close to host time - OK
‼ DNS server - Warning
Container engine is not configured with DNS server setting, which may impact connectivity to IoT Hub.
Please see https://aka.ms/iotedge-prod-checklist-dns for best practices.
You can ignore this warning if you are setting DNS server per module in the Edge deployment.
√ production readiness: logs policy - OK
√ production readiness: Edge Agent's storage directory is persisted on the host filesystem - OK
√ production readiness: Edge Hub's storage directory is persisted on the host filesystem - OK
√ proxy settings are consistent in aziot-edged, aziot-identityd, moby daemon and config.toml - OK

Connectivity checks
-------------------
27 check(s) succeeded.
4 check(s) raised warnings. Re-run with --verbose for more details.
7 check(s) were skipped due to errors from other checks. Re-run with --verbose for more details.

```

### Device Information
* Host OS [e.g. Ubuntu 18.04, Windows Server IoT 2019]: Ubuntu 20.09
* Architecture [e.g. amd64, arm32, arm64]: arm64
* Container OS [e.g. Linux containers, Windows containers]: Linux containers

### Runtime Versions
* aziot-edged [run `iotedge version`]: 1.4.1
* Edge Agent [image tag (e.g. 1.0.0)]: 1.4
* Edge Hub [image tag (e.g. 1.0.0)]: 1.4
* Docker/Moby [run `docker version`]: 20.10.18

Note: when using Windows containers on Windows, run `docker -H npipe:////./pipe/iotedge_moby_engine version` instead

## Logs

aziot-edged logs

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edge-agent logs

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edge-hub logs

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## Additional Information
Please provide any additional information that may be helpful in understanding the issue.