Summary

This PR removes the @ prefix from remote module references throughout the codebase. DSL include statements now use scope/name format instead of @scope/name. Local/built-in includes still require /, ./, ../, or plugin/ prefixes to be unambiguous.

Changes

Module reference format (scope/name)

• ModuleReference.groovy: Removed optional @? from MODULE_NAME_PATTERN; fullName no longer includes @
• IncludeDef.groovy: Remote module detection changed from startsWith('@') to absence of local prefixes + valid scope/name pattern validation via ModuleReference.parse()
• ModuleResolver.java (nf-lang): Replaced startsWith("@") with isRemoteModule(source) static helper that validates the scope/name regex pattern
• ResolveIncludeVisitor.java (nf-lang): isRemoteModule now delegates to ModuleResolver.isRemoteModule() for consistent pattern validation
• PipelineSpec.groovy: Backward-compat: strips leading @ when reading old nextflow_spec.json entries
• All CLI commands (CmdModuleInstall, CmdModuleRemove, CmdModuleInfo, CmdModuleRun): removed '@' + args[0] prepending; args[0] passed directly to ModuleReference.parse()

.checksum → .module-info properties file

• ModuleChecksum.groovy: Renamed CHECKSUM_FILE constant to MODULE_INFO_FILE = ".module-info". The file format changed from a raw checksum string to a Java properties file with a checksum=<sha256> entry. save() merges into existing properties; load() reads the checksum property
• InstalledModule.groovy: Renamed field checksumFile → moduleInfoFile; enum value MISSING_CHECKSUM → NO_REMOTE_MODULE
• ModuleStorage.groovy: Uses .module-info as the marker file when scanning modules/ for installed modules; skips .module-info when creating bundles
• ModuleRegistryClient.groovy: Simplified encodeName (no longer strips @)

Key Design Decisions

1. Folder modules/scope/name without .module-info → treated as "not a remote module"

When the resolver encounters a directory that exists at modules/scope/name but has no .module-info file, it means the folder was not installed via nextflow module install (e.g. a manually created or pre-existing local directory):

• Resolution (nextflow run): warns and continues (same behaviour as MODIFIED)
• Install (nextflow module install): fails with an error pointing to the existing folder and suggesting --force to override

2. nextflow module list does not show folders without .module-info

ModuleStorage.listInstalled() scans the modules/ tree and only recognises directories that contain a .module-info file. Folders without this marker are silently ignored. This means manually-created modules/scope/name directories are invisible to the module list command.

3. nextflow module publish scope/name creates/updates .module-info with the current checksum

When publishing a module using a module reference (scope/name), the publish command creates or updates the .module-info file with the current directory checksum. This marks the directory as a registered remote module and sets the integrity baseline.

Note for cherry-pick

Commit 3119155 contains only CLI changes (renaming subcommands) and is safe to cherry-pick to PR #6768.

Test plan

• nextflow module install nf-core/fastqc installs to modules/nf-core/fastqc/ with .module-info containing checksum=<sha256>
• nextflow module list shows only modules with .module-info; manual folders are not shown
• DSL include include { FASTQC } from 'nf-core/fastqc' resolves correctly
• DSL include include { FASTQC } from '@nf-core/fastqc' fails with a clear error
• nextflow module install on a folder without .module-info fails without --force
• Unit tests: make test module=nextflow passes

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