fix: load knowledge diffing after core types

[hyperpolymath]

KnowledgeDiffing defines methods over ResearchProject and LinkedEntity. Load that submodule after the core type definitions so package initialization succeeds.

[gitar-bot]

🚨 Bug: Load-order fix is incomplete; other submodules still fail

diffing.jl failed to load because it references ResearchProject/LinkedEntity in method signatures (evaluated at definition time) via using ..PostDisciplinary, while being included before those structs are defined at lines 80-96. But triangulation.jl (line 37), evolutionary.jl (38), hermeneutics.jl (40), and knowledge_transfer.jl (42) use the exact same pattern and are all still included before the type definitions. Since triangulation.jl now loads at the first include position that previously belonged to diffing.jl, package initialization will still throw UndefVarError: ResearchProject/LinkedEntity at triangulation.jl before diffing.jl is ever reached — the PR does not actually make the package load. Move the core type definitions (structs LinkedEntity, ResearchProject, and the ResearchProject(name) constructor) above the entire include(...) block so every submodule can resolve them, which also lets diffing.jl stay in place.

Hoist LinkedEntity/ResearchProject above all include() calls so all submodules load; keep full docstrings from the original definitions.:

# Define core public types BEFORE any include, so every submodule that
# references them in method signatures can resolve them at load time.
struct LinkedEntity
    id::UUID; source_library::Symbol; original_id::Symbol
    kind::Symbol; metadata::Dict{Symbol, Any}
end
struct ResearchProject
    id::Symbol; name::String; graph::MetaGraph
end
function ResearchProject(name::String)
    g = MetaGraph(SimpleGraph(); label_type=UUID, vertex_data_type=LinkedEntity,
                  edge_data_type=Dict{Symbol,Any}, graph_data=name)
    return ResearchProject(gensym("project"), name, g)
end
# ...then the include(...) block, including synthesis/diffing.jl

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⚠️ This PR is blocked due to unresolved code review findings.

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Code Review 🚫 Blocked 0 resolved / 1 findings

Restores module initialization order for knowledge diffing, but the fix is incomplete as other submodules still fail to load.

🚨 Bug: Load-order fix is incomplete; other submodules still fail

📄 src/PostDisciplinary.jl:31-43 📄 src/PostDisciplinary.jl:80-94 📄 src/PostDisciplinary.jl:151-154

diffing.jl failed to load because it references ResearchProject/LinkedEntity in method signatures (evaluated at definition time) via using ..PostDisciplinary, while being included before those structs are defined at lines 80-96. But triangulation.jl (line 37), evolutionary.jl (38), hermeneutics.jl (40), and knowledge_transfer.jl (42) use the exact same pattern and are all still included before the type definitions. Since triangulation.jl now loads at the first include position that previously belonged to diffing.jl, package initialization will still throw UndefVarError: ResearchProject/LinkedEntity at triangulation.jl before diffing.jl is ever reached — the PR does not actually make the package load. Move the core type definitions (structs LinkedEntity, ResearchProject, and the ResearchProject(name) constructor) above the entire include(...) block so every submodule can resolve them, which also lets diffing.jl stay in place.

Hoist LinkedEntity/ResearchProject above all include() calls so all submodules load; keep full docstrings from the original definitions.

# Define core public types BEFORE any include, so every submodule that
# references them in method signatures can resolve them at load time.
struct LinkedEntity
    id::UUID; source_library::Symbol; original_id::Symbol
    kind::Symbol; metadata::Dict{Symbol, Any}
end
struct ResearchProject
    id::Symbol; name::String; graph::MetaGraph
end
function ResearchProject(name::String)
    g = MetaGraph(SimpleGraph(); label_type=UUID, vertex_data_type=LinkedEntity,
                  edge_data_type=Dict{Symbol,Any}, graph_data=name)
    return ResearchProject(gensym("project"), name, g)
end
# ...then the include(...) block, including synthesis/diffing.jl

🤖 Prompt for agents

Code Review: Restores module initialization order for knowledge diffing, but the fix is incomplete as other submodules still fail to load.

1. 🚨 Bug: Load-order fix is incomplete; other submodules still fail
   Files: src/PostDisciplinary.jl:31-43, src/PostDisciplinary.jl:80-94, src/PostDisciplinary.jl:151-154

   `diffing.jl` failed to load because it references `ResearchProject`/`LinkedEntity` in method signatures (evaluated at definition time) via `using ..PostDisciplinary`, while being `include`d before those structs are defined at lines 80-96. But `triangulation.jl` (line 37), `evolutionary.jl` (38), `hermeneutics.jl` (40), and `knowledge_transfer.jl` (42) use the exact same pattern and are all still included before the type definitions. Since triangulation.jl now loads at the first include position that previously belonged to diffing.jl, package initialization will still throw `UndefVarError: ResearchProject`/`LinkedEntity` at triangulation.jl before diffing.jl is ever reached — the PR does not actually make the package load. Move the core type definitions (structs `LinkedEntity`, `ResearchProject`, and the `ResearchProject(name)` constructor) above the entire `include(...)` block so every submodule can resolve them, which also lets diffing.jl stay in place.

   Fix (Hoist LinkedEntity/ResearchProject above all include() calls so all submodules load; keep full docstrings from the original definitions.):
   # Define core public types BEFORE any include, so every submodule that
   # references them in method signatures can resolve them at load time.
   struct LinkedEntity
       id::UUID; source_library::Symbol; original_id::Symbol
       kind::Symbol; metadata::Dict{Symbol, Any}
   end
   struct ResearchProject
       id::Symbol; name::String; graph::MetaGraph
   end
   function ResearchProject(name::String)
       g = MetaGraph(SimpleGraph(); label_type=UUID, vertex_data_type=LinkedEntity,
                     edge_data_type=Dict{Symbol,Any}, graph_data=name)
       return ResearchProject(gensym("project"), name, g)
   end
   # ...then the include(...) block, including synthesis/diffing.jl

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