Apply input transformation to multi-protocol templates

[mhmdiaa]

Proposed changes

The multi-protocol execution engine does not apply input transformation as the generic engine does. This PR adds the transformation step to the multi-protocol engine to resolve #5425 and similar inconsistencies.

I have also removed the ad hoc transformers that were partially addressing the issue in the DNS and SSL engines. Let me know if you think this is the correct approach, as this causes two of the current tests to fail due to the transformation being handled at the outer layer.

Test template

id: test-multi-request-input-handling

info:
  name: Test Single Protocol Input Handling
  author: mhmdiaa
  severity: info

dns:
  - name: "{{FQDN}}"
    type: A
  - name: "{{FQDN}}"
    type: A

Before

nuclei -debug -u example.com:443 -t test-multi-request-input-handling.yaml
...
;; QUESTION SECTION:
;example.com:443.	IN	 A
...
;; opcode: QUERY, status: NXDOMAIN, id: 25391
...
;; QUESTION SECTION:
;example.com:443.	IN	 A
...
;; opcode: QUERY, status: NXDOMAIN, id: 22694

After

nuclei -debug -u example.com:443 -t test-multi-request-input-handling.yaml
...
;; QUESTION SECTION:
;example.com.	IN	 A
...
;; opcode: QUERY, status: NOERROR, id: 27821
...
;; ANSWER SECTION:
example.com.	92	IN	A	93.184.215.14
...
;; QUESTION SECTION:
;example.com.	IN	 A
...
;; opcode: QUERY, status: NOERROR, id: 28024
...
...
;; ANSWER SECTION:
example.com.	283	IN	A	93.184.215.14

Checklist

• Pull request is created against the dev branch
• All checks passed (lint, unit/integration/regression tests etc.) with my changes
• I have added tests that prove my fix is effective or that my feature works
• I have added necessary documentation (if appropriate)

[tarunKoyalwar]

lgtm !

tests are flaky works fine locally

[tarunKoyalwar]

@mhmdiaa thanks for contributing , i updated the tests and some other outdated code and added this in flow templates as well , nice catch !

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