Remove deprecated qubit auto-alignment

[Adithyaphani]

###Summary:

Issue #1024 fix
Removes the automatic qubit padding behavior from the helper utilities and cleans up deprecated logic related to qubit derivation.
This PR updates the helper behavior to make qubit handling stricter and more explicit by avoiding silent circuit modifications.

###Details and comments:

Removed the automatic qubit padding mechanism from the helper:
Deleted deprecated logic from derive_num_qubits
Updated the helper to raise an explicit error instead of silently padding circuits
Improves transparency and prevents unexpected circuit behavior during execution
Simplifies the internal qubit-handling flow and removes deprecated pathways This change may affect workflows that previously relied on implicit circuit padding behavior.

[CLAassistant]

All committers have signed the CLA.

[Adithyaphani]

@edoaltamura @adekusar-drl @oscar-wallis @OkuyanBoga looking forward to your reviews on the given PR .Happy to make further changes and developments .

[Adithyaphani]

@oscar-wallis @OkuyanBoga @edoaltamura @adekusar-drl looking forward to your review on PR and response from your side.

[Adithyaphani]

Hey @oscar-wallis @OkuyanBoga @edoaltamura @adekusar-drl looking forward to your review on PR and response from your side. Can you please review this PR and I'm happy to make further changes if needed.

[oscar-wallis]

Hi @Adithyaphani , I'm on this, sorry for the delay!

[Adithyaphani]

Okay @oscar-wallis

[oscar-wallis]

Hi @Adithyaphani , could you check over our new AI Policy and confirm you have read and understood it? In line with the new AI Policy, please also disclose whether or not you used AI in this PR and if so, which? A similar message is being sent to all open PRs.

[Adithyaphani]

@oscar-wallis the usage of AI was only up to helping few nitty-gritty points of issue and PR description part. But the logic and code part is done by myself. Looking forward to your response and happy to make further changes if needed.

[coveralls]

Coverage Report for CI Build 31481790807

Coverage decreased (-0.03%) to 89.764%

Details

• Coverage decreased (-0.03%) from the base build.
• Patch coverage: 14 of 14 lines across 1 file are fully covered (100%).
• 1 coverage regression across 1 file.

Uncovered Changes

No uncovered changes found.

Coverage Regressions

1 previously-covered line in 1 file lost coverage.

File	Lines Losing Coverage	Coverage
qiskit_machine_learning/utils/deprecation.py	1	40.0%

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Coverage Stats

Relevant Lines:	5979
Covered Lines:	5367
Line Coverage:	89.76%
Coverage Strength:	0.9 hits per line

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💛 - Coveralls

[Adithyaphani]

@oscar-wallis Pushed 131f4ad to fix the coverage regression on deprecation.py.

This PR removes the qubit auto-alignment code from adjust_num_qubits.py, which was the only path in the test suite exercising issue_deprecation_msg() — dropping the file's coverage to 40%. Added test/utils/test_deprecation.py covering issue_deprecation_msg, deprecate_function, and deprecate_arguments directly. Locally: 5/5 passing, 100% coverage on the file.

Note: deprecate_function/deprecate_arguments are actually unused dead code repo-wide — tested them here for coverage, but happy to remove instead in a follow-up if preferred.

[Adithyaphani]

@oscar-wallis Looking forward to your review and happy to make further changes if needed.

[Adithyaphani]

@oscar-wallis looking forward to your response and happy to make further changes if needed.

[Adithyaphani]

@oscar-wallis looking forward to your response and happy to make further changes if needed. Are you further looking to move forward with this issue or not?

[Adithyaphani]

@oscar-wallis and @OkuyanBoga and @garrison looking forward to your review on this PR. Would like to make further changes if needed.