refactor: replace some references with owned structures in VMLogic

[nagisa]

VMLogic containing a lifetime makes it difficult to have it live for any longer than a short sequence of instantiate-link-run and is one of the reasons why we're forced to have some unsafe code in our linking code.

This refactor replaces some of the reference fields with Arcs, Boxes, etc. This is not a complete refactor, I intend to do the remainder as a follow-up.

Based on #11614 Part of #11319

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 79.09605% with 37 lines in your changes missing coverage. Please review.

Project coverage is 71.45%. Comparing base (8189888) to head (4851fce).

Files	Patch %	Lines
...ntime/runtime-params-estimator/src/gas_metering.rs	55.55%	16 Missing :warning:
runtime/near-vm-runner/src/wasmer_runner.rs	27.27%	0 Missing and 8 partials :warning:
...time/runtime-params-estimator/src/function_call.rs	52.94%	8 Missing :warning:
...me-params-estimator/src/costs_to_runtime_config.rs	0.00%	4 Missing :warning:
runtime/runtime/src/lib.rs	85.71%	0 Missing and 1 partial :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #11615 +/- ## ========================================== - Coverage 71.48% 71.45% -0.03% ========================================== Files 788 788 Lines 160835 160921 +86 Branches 160835 160921 +86 ========================================== + Hits 114968 114993 +25 - Misses 40850 40901 +51 - Partials 5017 5027 +10 ``` | [Flag](https://app.codecov.io/gh/near/nearcore/pull/11615/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=near) | Coverage Δ | | |---|---|---| | [backward-compatibility](https://app.codecov.io/gh/near/nearcore/pull/11615/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=near) | `0.23% <0.00%> (-0.01%)` | :arrow_down: | | [db-migration](https://app.codecov.io/gh/near/nearcore/pull/11615/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=near) | `0.23% <0.00%> (-0.01%)` | :arrow_down: | | [genesis-check](https://app.codecov.io/gh/near/nearcore/pull/11615/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=near) | `1.35% <0.00%> (-0.01%)` | :arrow_down: | | [integration-tests](https://app.codecov.io/gh/near/nearcore/pull/11615/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=near) | `37.66% <37.85%> (-0.02%)` | :arrow_down: | | [linux](https://app.codecov.io/gh/near/nearcore/pull/11615/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=near) | `68.89% <78.53%> (+0.01%)` | :arrow_up: | | [linux-nightly](https://app.codecov.io/gh/near/nearcore/pull/11615/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=near) | `70.94% <79.09%> (-0.04%)` | :arrow_down: | | [macos](https://app.codecov.io/gh/near/nearcore/pull/11615/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=near) | `52.29% <67.14%> (-0.28%)` | :arrow_down: | | [pytests](https://app.codecov.io/gh/near/nearcore/pull/11615/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=near) | `1.58% <0.00%> (-0.01%)` | :arrow_down: | | [sanity-checks](https://app.codecov.io/gh/near/nearcore/pull/11615/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=near) | `1.38% <0.00%> (-0.01%)` | :arrow_down: | | [unittests](https://app.codecov.io/gh/near/nearcore/pull/11615/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=near) | `66.12% <74.57%> (-0.03%)` | :arrow_down: | | [upgradability](https://app.codecov.io/gh/near/nearcore/pull/11615/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=near) | `0.28% <0.00%> (-0.01%)` | :arrow_down: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=near#carryforward-flags-in-the-pull-request-comment) to find out more.

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