- Remove integrate.jl (no longer needed)
- Remove solve_system.jl and solve_vector_field.jl (simplified to solve(flow, config))
- Remove test_integrate.jl (no longer needed)
- Update Pipelines.jl manifest

- Add RecipesBase to deps and Plots to weakdeps
- Add CTFlowsPlotsExt extension with plot, plot! methods
- Add RecipesBase.plot stub in solution.jl (throws error if extension not loaded)
- Move RecipesBase import to Systems.jl module level
- Remove callable stub (not needed for extension)
- Update example script to use new API

- Remove callable stub from solution.jl
- Add actual callable directly in solution.jl (delegates to sol.raw)
- Remove callable from CTFlowsPlotsExt.jl (not Plots-specific)
- Callable is always available since it just delegates to raw SciML solution

- Add comprehensive docstring for AbstractTag explaining its role as a dispatch tag for extension architecture
- Update docstrings.md to clarify that internal references (@ref) must use full module path including root package
- Fix templates to show proper qualification pattern (PackageName.ModuleName.symbol)

…tion

- Add docstrings for PointConfig and TrajectoryConfig structs
- Add docstring for AbstractTag explaining dispatch-based extension architecture
- Fix api_reference.jl: replace Core with Common, remove ADBackends and Modelers
- Update index.md to remove references to non-existent modules
- Update docstrings.md to clarify @ref qualification requires full module path

- Add AbstractConfig abstract type as marker for configuration objects
- Update PointConfig and TrajectoryConfig to subtype AbstractConfig
- Export AbstractConfig from Common module
- Type config parameters with Common.AbstractConfig in:
  - AbstractFlow callable signature
  - Systems.ode_problem signature
  - Systems.build_solution signature
  - Pipelines.solve signature
- Update docstring cross-references to use full module path

…andards

- Add tests for AbstractConfig export verification
- Add tests for type hierarchy (PointConfig/TrajectoryConfig <: AbstractConfig)
- Add tests for Base.show methods for both config types
- Follow testing standards with clear section separation and descriptive test names

…eferences

- Update all internal cross-references to use full module path with root package
- Fix contract section examples to use CTFlows.Common.PointConfig and CTFlows.Common.TrajectoryConfig
- Update See also sections to use CTFlows.Flows.Flow, CTFlows.Systems.AbstractSystem, CTFlows.Integrators.AbstractODEIntegrator

- Add (f::FakeFlow)(config::Common.AbstractConfig) method
- Add test for callable with TrajectoryConfig on MinimalFlow
- Add test for callable with config on FakeFlow (PointConfig and TrajectoryConfig)
- Add exception message verification using try-catch blocks
- Ensure all NotImplemented exceptions are tested with fake structs

Let exceptions propagate naturally when contract methods are not implemented,
forcing proper implementation rather than silently hiding errors.

- Update cross-references to use full module path
- Add # Arguments and # Returns sections to all function docstrings
- Improve documentation for system, integrator, and callable methods

- Add docstrings to PointConfig show methods
- Add docstrings to TrajectoryConfig show methods
- Add docstrings to specialized Flow show methods for VectorFieldSystem

- Add Real type constraints to PointConfig (T0, TF) and TrajectoryConfig (TS)
- Add tspan accessor functions for both config types for consistent API
- Add docstrings to tspan functions with examples
- Generalize __autonomous and __variable docstrings to apply to all time-dependent objects (not just VectorField)

… file

- Add tspan to Common.jl exports (was missing)
- Create test_abstract_tag.jl for abstract_tag.jl
- Create test_configs.jl for configs.jl (with fake types for contract testing)
- Create test_default.jl for default.jl
- Rename test_common.jl to test_traits.jl (tests for traits.jl only)
- Create test_common_module.jl to verify Common.jl exports and type hierarchy
- Remove duplicate configs tests from test_common.jl

Each source file now has its own orthogonal test file following testing standards.

- Add _caller_function_name() to detect caller from stacktrace instead of requiring source_method argument
- Update has_time_dependence_trait and has_variable_dependence_trait to use automatic caller detection
- Remove source_method argument from all accessor functions (is_autonomous, is_nonautonomous, is_variable, is_nonvariable, has_variable)
- Update has_variable docstring to reflect it's no longer an alias
- Add test_error_contains_caller helper function for testing error messages
- Fix _caller_function_name to skip exact trait check function names (has_time_dependence_trait, has_variable_dependence_trait)
- Update trait tests to use === instead of isa for type comparisons
- All tests pass (52/52)

- Add Example sections to all docstrings in abstract_system.jl
  - Show concrete MySystem implementation for contract methods
  - Return trait types (not instances) in examples
  - Add usage examples for rhs! function

- Revise test_abstract_system.jl to be orthogonal
  - Remove tests for methods not in abstract_system.jl
  - Add trait method tests (has_time_dependence_trait, has_variable_dependence_trait)
  - Add logic tests for rhs! signature and behavior
  - Add NotImplemented error structure verification
  - Fix DataType tests (not supported by trait methods)
  - Fix NotImplemented error test (use try/catch instead of @test_throws)

- Add docstrings for VectorField struct, constructor, trait methods, and Base.show
- Add trait methods (has_time_dependence_trait, has_variable_dependence_trait)
- Add docstrings for time_dependence and variable_dependence with examples
- Fix VectorField type parameter to F<:Function
- Fix time_dependence and variable_dependence to use Common. prefix
- Revise test_vector_field.jl to be orthogonal (only test vector_field.jl)
- Remove tests for VectorFieldSystem (move to separate file)
- Remove tests for non-existent explicit constructor
- Add tests for trait methods and trait checks
- Add tests for natural call signatures (scalar, vector, matrix)
- Add tests for uniform call signature (t, x, v)
- Add tests for Common trait predicates (is_autonomous, is_variable, etc.)
- Fix VectorFieldSystem type parameter to F<:Function
- Fix matrix test expectations

- Add example and See also to VectorFieldSystem struct docstring
- Add Arguments, Returns, Example, See also to rhs! docstring
- Add Example and See also to variable_dependence docstring
- Add Example and See also to time_dependence docstring
- Add docstrings for Base.show methods
- Create test_vector_field_system.jl with orthogonal tests
- Test Abstract Types, Construction, Contract Implementation
- Test trait methods and Common trait predicates
- Add exports verification

- Create new Data submodule with VectorField type
- Move vector_field.jl from Systems/ to Data/
- Update all references from Systems.VectorField to Data.VectorField
- Add Data module to CTFlows.jl in correct order (Common → Data → Systems)
- Update Systems.jl to import Data module
- Update Pipelines.jl to import Data module
- Move build_solution.jl and solution.jl from Systems/ to Pipelines/
- Create test_data_module.jl for Data module exports
- Create test_systems_module.jl for Systems module exports
- Remove test_vector_field.jl from test/suite/systems/

- Add missing docstrings for trait methods (has_time_dependence_trait, has_variable_dependence_trait, time_dependence)
- Improve AbstractFlow docstring with Traits section explaining delegation to system
- Improve variable_dependence docstring with arguments and returns
- Remove irrelevant callable method tests (not part of AbstractFlow contract)
- Fix FakeSystem to implement correct AbstractSystem contract
- Add CTFlows.Data import for VectorField integration tests
- Update VectorField constructor calls to use kwargs (autonomous, variable)
- All tests now pass (40/40)

…actFlow

- Add VD<:Common.VariableDependence parameter to AbstractSystem{VD}
- Add VD<:Common.VariableDependence parameter to AbstractFlow{VD}
- Update Flow{VD, S, I} to inherit VD from system type
- Simplify Flow callable methods: use variable=nothing instead of trait-based dispatch
- Remove error-throwing methods for Fixed/NonFixed variable handling
- Update VectorFieldSystem to subtype AbstractSystem{VD}
- Add test_flow_module.jl for Flows module exports verification
- Update docstrings for Flow callable methods with See also sections

…ture

- Fix system(f::Flow{VD, S, I}) and integrator(f::Flow{VD, S, I}) signatures to include VD parameter
- Update test_abstract_flow.jl: FakeSystem and FakeFlow to subtype parametric types
- Update test_flow.jl: FakeSystem/FakeFlow to use Common.Fixed/Common.NonFixed types
- Update test_flow_module.jl: FakeSystem to subtype AbstractSystem{Common.Fixed}
- Update trait implementations to return types (Common.Fixed) instead of instances (Common.Fixed())
- Remove trait-based dispatch error tests (now using variable=nothing pattern)

- Add Flows.building.jl: high-level Flow constructor from VectorField
- Add Flows.calling.jl: call function for solving ODE problems with helpers
- Add Systems.building.jl: build_system function for VectorFieldSystem
- Add Integrators.building.jl: build_integrator function for integrator creation
- Add comprehensive tests for building.jl in Systems and Flows modules
- Add comprehensive tests for calling.jl using fake structs
- Update Flows.jl exports: add call to public API
- Add docstrings to all new functions following project standards
- Rename AbstractODEIntegrator to AbstractIntegrator throughout
- Remove Pipelines module (functionality moved to Flows)
- Update Project.toml: remove OrdinaryDiffEqTsit5 from test dependencies
- Update Integrators exports: AbstractIntegrator instead of AbstractODEIntegrator
- Update Flows exports: add call function

- Rename abstract_ode_integrator.jl to abstract_integrator.jl for consistency
- Fix contract documentation: remove Base.show and describe (not part of required contract)
- Reorganize contract into type-level (id, metadata) and instance-level (options) sections
- Document all three required callable signatures: problem building, integration, solution building
- Add default NotImplemented implementations for all three callables
- Update tests to verify all three callable signatures
- Fix parametric type issue in FakeSystem (AbstractSystem{Common.Fixed})

- Add TD parameter to AbstractSystem{TD, VD} with TD before VD
- Move time_dependence and variable_dependence methods to AbstractSystem abstract type
- Update VectorFieldSystem to match new AbstractSystem signature
- Add TD parameter to AbstractFlow{TD, VD} and Flow{TD, VD, S, I}
- Update Flow calling.jl to handle TD parameter
- Add initial_condition method to Common module for normalizing initial conditions
- Update all test files to use new TD-before-VD signature
- Remove redundant trait methods from concrete types

… HSYS variants

…rge HSYS variants

…solidate HSYS variants

…nsion

…ispatch

…est_sciml_extension.jl

…trix-forms-adaptive

Feature/scalar vector matrix forms adaptive

- Add __hvf_inplace()::Bool = false to src/Common/default.jl
- Export __hvf_inplace from src/Common/Common.jl
- Add test for __hvf_inplace in test/suite/common/test_default.jl

…_vector_field getter

- Add __ad_backend() returning AutoForwardDiff() to src/Differentiation/building.jl
- Add ad_backend_type contract stub to src/Differentiation/abstract_ad_backend.jl
- Add ad_backend_type concrete impl for DifferentiationInterface to src/Differentiation/differentiation_interface.jl
- Export __ad_backend and ad_backend_type from src/Differentiation/Differentiation.jl

…or_field getter

- Add __ad_backend() returning AutoForwardDiff() to src/Differentiation/building.jl
- Add ad_backend contract stub to src/Differentiation/abstract_ad_backend.jl
- Add ad_backend concrete impl for DifferentiationInterface to src/Differentiation/differentiation_interface.jl
- Export __ad_backend and ad_backend from src/Differentiation/Differentiation.jl

- Add src/Systems/hamiltonian_getter.jl with 8 closure factories (4 OOP + 4 IP)
  and 4 getter overloads (Hamiltonian, HamiltonianVectorFieldSystem, 
  HamiltonianSystem, AbstractHamiltonianSystem stub)
- Modify src/Systems/Systems.jl to include hamiltonian_getter.jl and export
  hamiltonian_vector_field (removed unused ADTypes import)
- Add test/suite/systems/test_hamiltonian_getter.jl with 85 tests covering:
  - Contract tests (ad_backend stub, AbstractHamiltonianSystem stub)
  - Structure tests with mocks (all 4 TD×VD cases)
  - Trivial getter for HamiltonianVectorFieldSystem
  - Real OOP tests with DifferentiationInterface (5 cases including variable_costate)
  - Real IP tests with DifferentiationInterface (4 cases)
  - Traits verification (8 cases: 4 OOP + 4 IP)
  - HamiltonianSystem structure tests (4 missing cases)
  - Export test
- All tests pass (85/85)

…nFlow

- Add Systems.hamiltonian_vector_field overloads for HamiltonianFlow with HamiltonianSystem and HamiltonianVectorFieldSystem
- Import and re-export hamiltonian_vector_field from Flows module
- Add comprehensive tests for flow-level delegation covering all trait combinations
- Tests organized as UNIT (trait preservation), INTEGRATION (delegation by trait), CONTRACT (identity), and EXPORTS

…ions

- Add detailed docstrings to 8 internal closure factory functions (_make_oop_hvf, _make_ip_hvf)
- Add comprehensive docstrings to 4 public system-level getter overloads
- Add detailed docstrings to 2 flow-level getter overloads
- Follow CTFlows documentation standards with TYPEDSIGNATURES, Arguments, Returns, Notes, and cross-references

…guards

- Data layer: expanded 4 NonFixed call signatures (OOP/IP) to accept variable_costate kwarg with hasmethod guard throwing PreconditionError when inner f doesn't support it
- Systems layer: added dpv and variable_costate kwargs to 2 IP NonFixed closure factories with PreconditionError guard when dpv===nothing
- Updated IP NonFixed docstrings to reflect implementation
- Added 3 testsets for Data layer (user-built HVF error handling)
- Added 8 testsets for Systems layer (IP variable_costate, hasmethod detection, OOP default)
- Full suite verification: 2382 tests pass

Feature/hvf getter