Review present in BIDS 2.0 deprecations and handle them

[yarikoptic]

there are already dedicated issues some of which might have been "implemented" in BIDS 1.0 and just need to be really removed from BIDS spec and potentially provided automated migration, e.g.

• Remove deprecated suffixes (e.g. FLASH, phase, etc) Was: Change FLASH for non-proprietary name #5

looking at src of bids we find that some are already encoded in the schema and its rules, and I think should be trimmed entirely

git grep -i deprecated -- src

src/CHANGES.md:-   \[FIX] Add deprecated anatomical MRI suffixes back into schema [#725](https://github.com/bids-standard/bids-specification/pull/725) ([tsalo](https://github.com/tsalo))
src/appendices/coordinate-systems.md:-   The use of `ElektaNeuromag` is [DEPRECATED][deprecated]. Dataset curators SHOULD use `NeuromagElektaMEGIN` instead.
src/appendices/coordinate-systems.md:However, their use is [DEPRECATED][deprecated].
src/appendices/coordinate-systems.md:[deprecated]: ../common-principles.md#definitions
src/appendices/qmri.md:      "BasedOn": "DEPRECATED",
src/common-principles.md:Bare DOIs such as `10.18112/openneuro.ds000001.v1.0.0` are [DEPRECATED][].
src/common-principles.md:[deprecated]: #definitions
src/derivatives/common-data-types.md:| [URI][]   | This can be used to point to a specific file. Paths written relative to the root of the derivative dataset are [DEPRECATED][] in favor of [BIDS URIs][]. |
src/derivatives/common-data-types.md:[deprecated]: ../common-principles.md#definitions
src/metaschema.json:        "enum": ["required", "recommended", "optional", "deprecated"]
src/modality-specific-files/magnetic-resonance-imaging-data.md:### Deprecated suffixes
src/modality-specific-files/magnetic-resonance-imaging-data.md:1.5.0 have been deprecated.
src/modality-specific-files/magnetic-resonance-imaging-data.md:(`_phase`) data, but the `_phase` suffix is [deprecated](../common-principles.md#definitions).
src/schema/README.md:BIDS also defines a level `DEPRECATED`, rendered in the schema as `deprecated`,
src/schema/README.md:| `level`      | Requirement level of file, one of (`optional`, `recommended`, `required`, `deprecated`)                       |
src/schema/README.md:| `level`      | Requirement level of file, one of (`optional`, `recommended`, `required`, `deprecated`)                           |
src/schema/README.md:| `level`  | REQUIRED          | Requirement level of field, one of (`optional`, `recommended`, `required`, `deprecated`) |
src/schema/README.md:| `level`                | REQUIRED          | Requirement level of field, one of (`optional`, `recommended`, `required`, `deprecated`) |
src/schema/objects/common_principles.yaml:deprecated:
src/schema/objects/common_principles.yaml:  display_name: DEPRECATED
src/schema/objects/common_principles.yaml:    A "deprecated" entity or metadata field SHOULD NOT be used in the generation of new datasets.
src/schema/objects/common_principles.yaml:    Validating software SHOULD warn when deprecated practices are detected
src/schema/objects/enums.yaml:    - $ref: objects.enums.ElektaNeuromag.value # deprecated
src/schema/objects/enums.yaml:_StandardTemplateDeprecatedCoordSys:
src/schema/objects/enums.yaml:    [DEPRECATED](SPEC_ROOT/common-principles.md#definitions).
src/schema/objects/metadata.yaml:    - $ref: objects.enums._StandardTemplateDeprecatedCoordSys
src/schema/objects/metadata.yaml:    [DEPRECATED](SPEC_ROOT/common-principles.md#definitions).
src/schema/objects/metadata.yaml:    This field is DEPRECATED, and this metadata SHOULD be recorded in the
src/schema/objects/metadata.yaml:    [DEPRECATED](SPEC_ROOT/common-principles.md#definitions).
src/schema/objects/metadata.yaml:    - $ref: objects.enums._StandardTemplateDeprecatedCoordSys
src/schema/objects/metadata.yaml:    - $ref: objects.enums._StandardTemplateDeprecatedCoordSys
src/schema/objects/metadata.yaml:    - $ref: objects.enums._StandardTemplateDeprecatedCoordSys
src/schema/objects/metadata.yaml:    - $ref: objects.enums._StandardTemplateDeprecatedCoordSys
src/schema/objects/metadata.yaml:    [DEPRECATED](SPEC_ROOT/common-principles.md#definitions).
src/schema/objects/metadata.yaml:    [DEPRECATED](SPEC_ROOT/common-principles.md#definitions).
src/schema/objects/metadata.yaml:    - $ref: objects.enums._StandardTemplateDeprecatedCoordSys
src/schema/objects/metadata.yaml:    - $ref: objects.enums._StandardTemplateDeprecatedCoordSys
src/schema/objects/metadata.yaml:    This field is DEPRECATED, and this metadata SHOULD be recorded in the
src/schema/objects/metadata.yaml:    This field is DEPRECATED, and this metadata SHOULD be recorded in the `acq_time` column of the
src/schema/objects/metadata.yaml:    [DEPRECATED](SPEC_ROOT/common-principles.md#definitions).
src/schema/objects/metadata.yaml:    - $ref: objects.enums._StandardTemplateDeprecatedCoordSys
src/schema/objects/suffixes.yaml:    [DEPRECATED](SPEC_ROOT/common-principles.md#definitions).
src/schema/rules/checks/deprecations.yml:    code: ELEKTA_NEUROMAG_DEPRECATED
src/schema/rules/checks/deprecations.yml:        "ElektaNeuromag" as a coordinate system is deprecated.
src/schema/rules/checks/func.yaml:PhaseSuffixDeprecated:
src/schema/rules/checks/func.yaml:    code: PHASE_SUFFIX_DEPRECATED
src/schema/rules/checks/func.yaml:      DEPRECATED. Phase information associated with magnitude information stored in BOLD contrast.
src/schema/rules/common_principles.yaml:- deprecated
src/schema/rules/files/raw/anat.yaml:    - T2star # deprecated
src/schema/rules/files/raw/anat.yaml:    - FLASH # deprecated
src/schema/rules/files/raw/anat.yaml:    - PD # deprecated
src/schema/rules/files/raw/func.yaml:    - phase # deprecated
src/schema/rules/sidecars/derivatives/common_derivatives.yaml:    RawSources: deprecated
src/schema/rules/sidecars/derivatives/common_derivatives.yaml:    RawSources: deprecated
src/schema/rules/sidecars/ieeg.yaml:    DCOffsetCorrection: deprecated
src/schema/rules/sidecars/meg.yaml:        [DEPRECATED](SPEC_ROOT/common-principles.md#definitions).
src/schema/rules/sidecars/mri.yaml:    HardcopyDeviceSoftwareVersion: deprecated
src/schema/rules/sidecars/pet.yaml:      level: deprecated

potential other deprecations which would need more work to be implemented:

• Deprecate phase and magnitude suffixes in favor of part and echo entities for field maps #3