Unify pipeline warning/error reporting into PipelineMessages module

[joehendrix]

Consolidate WarningKind/SpecError into a new PipelineMessages module with typed phases, impact levels, and structured output. Callers now receive warnings in the result rather than having them printed to stderr.

Motivation

The pySpecLaurel pipeline previously mixed exception-based error handling (EIO String) with ad-hoc warning printing. This made it impossible to:

• Report all errors/warnings at once (exceptions abort on first failure)
• Attach source locations to pipeline errors
• Let callers control output format (JSON, summary, silent)

This PR establishes structured warning infrastructure as a foundation for end-to-end robust warning reporting across the full pipeline.

Design: impact drives behavior

Each MessageKind has a MessageImpact that determines pipeline behavior via isFatal:

Impact	Fatal?	Meaning
configurationError	yes	Invalid arguments or unreadable on-disk pyspecs
internalError	yes	Unexpected failure preventing output (e.g., name collision)
internalWarning	no	Unexpected condition that didn't prevent output
knownLimitation	no	Documented gap in modeling
userCodeIssue	no	Issue in the user's Python source

Architecture

PipelineM is a StateT PipelineState BaseIO monad where PipelineState carries:

• messages : Array PipelineMessage — all warnings and errors with source locations
• shouldAbort : Bool — set automatically when a fatal message is emitted

There may be multiple fatal errors collected (e.g., listing every missing module, not just the first).

Output changes

pythonAndSpecToLaurel returns BaseIO PythonToLaurelResult (.success program warnings or .failure error warnings). Callers invoke PipelineMessage.printSummary / writeSummaryJson explicitly.

JSON warning summary gains "impact" field:

{"phase": "pySpecToLaurel", "category": "unsupportedUnion", "impact": "knownLimitation", "count": 3}

Other changes

• resolveModules combinator deduplicates three resolve-and-iterate loops
• Name collision checks use first-wins with dedup, report all collisions with source locations
• Phase has phaseNumber for display ordering and a private constructor
• FunctionOverloads.paramName changed from Option String to String
• Specs/Error.lean deleted; extract reportUserCodeError helper in StrataMain

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[tautschnig]

verboseWarnings : Bool := false is a hardcoded constant — there's no way for users to enable verbose warnings without editing source code. This should either be:

1. A CLI flag (e.g., --verbose-pyspec-warnings) passed through to pythonAndSpecToLaurel, or
2. Controlled by the existing --verbose flag that's already available in the pipeline

The existing quiet parameter already suppresses the count line. Adding a verbose parameter (or reusing the one from the caller) would be cleaner than a dead constant.