Refactor rules to remove some false positives

[sshenzha]

• Audit-driven false-positive sweep across joins/, data_quality/, anti_patterns/, and concept_standardization/, plus one new rule and a small UI MCP improvement (a pill that shows if the MCP is on/off).

[Copilot]

Pull request overview

This PR focuses on reducing audit-identified false positives across multiple SQL validation rules by making table/alias resolution more scope-aware (especially around CTE shadowing), adds a new anti-pattern rule for CTE names that collide with OMOP tables, and includes a small UI enhancement showing MCP mount status.

Changes:

• Add anti_patterns.cte_shadows_omop_table and supporting helper collect_cte_names, plus tests and changelog updates.
• Refine multiple rules to avoid false positives: CTE-shadow-aware has_table_reference, scope-aware alias resolution (schema validation / OMOP_149), LIMIT scalar-aggregate carve-out, visit-occurrence join-key gating, and IN-subquery CTE bridging for join-path validation.
• UI: add an MCP on/off “pill” backed by the app’s live mcp_mounted state.

Reviewed changes

Copilot reviewed 16 out of 16 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
tests/test_rules.py	Adds regression tests for CTE shadowing, alias scoping, scalar-aggregate LIMIT carve-out, visit join-key gating, and new rule coverage.
tests/test_patch.py	Extends canonical suggested-fix verbs to include RENAME:.
tests/test_helpers_cte.py	Adds focused tests for new CTE-aware helper behavior.
src/fastssv/rules/joins/visit_occurrence_inner_join_validation.py	Gates OMOP_043 warnings on whether visit_occurrence_id is actually used in the join criteria.
src/fastssv/rules/joins/left_join_then_where_on_right_table.py	Refactors OMOP_149 to evaluate LEFT-join/right-table filters per-SELECT scope to avoid cross-CTE leakage.
src/fastssv/rules/joins/join_path_validation.py	Suppresses join-path warnings for canonical IN (SELECT ... FROM <vocab_cte>) cohort-builder bridging.
src/fastssv/rules/data_quality/comprehensive_schema_validation.py	Makes column resolution scope-aware and skips sqlglot time-unit keywords parsed as Column nodes.
src/fastssv/rules/concept_standardization/standard_concept_enforcement.py	Makes suggested-fix messaging CTE-shadow-aware (schema-qualified fix under shadow).
src/fastssv/rules/anti_patterns/limit_without_order_by.py	Adds scalar-aggregate detection to suppress LIMIT-without-ORDER-BY warnings for single-row aggregates.
src/fastssv/rules/anti_patterns/cte_shadows_omop_table.py	New anti-pattern rule warning on CTE names that shadow OMOP CDM tables.
src/fastssv/rules/anti_patterns/init.py	Exposes the new anti-pattern rule via package imports/__all__.
src/fastssv/core/helpers.py	Adds collect_cte_names and makes has_table_reference CTE-shadow-aware.
src/fastssv/api/ui.py	Adds MCP mount-status fields to the UI template context.
src/fastssv/api/templates/index.html	Renders an MCP on/off status pill.
src/fastssv/api/static/style.css	Styles the MCP status pill.
CHANGELOG.md	Documents the new rule and multiple false-positive reductions/fixes.

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[vvcb]

Should this apply to sub queries as well as CTEs?

[sshenzha]

Should this apply to sub queries as well as CTEs?

yes, good catch. I have extended it

[Copilot]

Pull request overview

Copilot reviewed 16 out of 16 changed files in this pull request and generated 2 comments.