Fix staging of Path fields of included record types

[robsyme]

Fixes #7225

Problem

When a typed process (nextflow.enable.types = true) declares an input whose type is a record included from another module file, the implicit stageAs directives for the record's Path fields are not generated. The fields are interpolated into .command.sh as raw source paths instead of staged paths. On a shared local filesystem the raw path still resolves, which masks the bug, but on an object-store work dir (e.g. Fusion/S3) the task fails with No such file or directory.

Isolating the variables with the reproducer shows the trigger is the record type being included from a separate file (the nextflow.enable.moduleBinaries flag suspected in the original report is unrelated):

Record definition	Field staged?
included from types.nf	no — raw source path
inline in main.nf	yes — TaskPath

Cause

ScriptCompiler performs resolution and Groovy conversion per source file, and the entry script is analyzed before the modules it includes. When ProcessToGroovyVisitorV2 inspects a record input to infer the implicit file inputs, the included record node is found (isRecordType is true) but its field types are still unresolved ClassNodes, so isPathType returns false and no stager is generated for the Path fields. The unstaged field then bypasses the staged-path substitution in TaskInputResolver.normalizeValue and reaches the task script as a raw source path.

Solution

• ModuleResolver now records the include dependencies of each source file, returning existing source units on repeat encounters so the dependency graph is complete.
• ScriptCompiler analyzes each source file only after the modules it includes from, so included types are fully resolved before they are used. Guards handle include cycles and unparseable modules.

Verification

• New unit test ScriptLoaderV2Test."should stage path fields of an included record type" fails before the change (0 file inputs generated) and passes after (2 file inputs).
• The issue reproducer (https://github.com/robsyme/nf-record-fusion-repro) now renders the record fields as staged TaskPath names instead of raw paths.
• Transitive includes (process in module A consuming a record included from module B) also stage correctly.
• Circular includes still fail with a StackOverflowError, but this is pre-existing behavior at runtime module loading (IncludeDef.loadModuleV2), unchanged by this PR.

🤖 Generated with Claude Code

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