Safer install/migrate bootstrap: index fixes, multi-root handling, and validation improvements

[Sendipad]

Motivation

• Prevent runtime and migration issues by moving DDL to migrate/patch flows and making bootstrap idempotent and defensive.
• Fix incorrect index column choices and fragile SQL generation that caused failed index creation on medium/large ledgers.
• Avoid creating erroneous single-root assumptions for Party Master when setup templates may intentionally create multiple roots.
• Harden settings validation to provide clearer errors and avoid frappe.get_meta() misuse.

Description

• Add docs/codebase_audit.md with audit notes and recommendations about which bootstraps belong to migrate vs install flows.
• Introduce include_schema_ddl flag to _safe_setup_operations() and call it with False from install paths and True from on_migrate() to ensure create_custom_indices() runs only during migrate/patch flows.
• Restrict create_gender_fixtures() to test or developer mode by checking frappe.flags.in_test or frappe.conf.get("developer_mode").
• Correct index definitions in create_custom_indices() to use customer for Sales Invoice and supplier for Purchase Invoice, verify existence of all referenced columns, quote column names in generated DDL, and log errors on failure.
• Make create_party_master_tree() tolerant of multi-root setups by only bootstrapping a fallback root when no roots exist and normalize an existing 1000 record when present.
• Improve PartyMasterSettings.validate_document_types() to require document_type with a row-specific error message and streamline parent/child validation logic.

Testing

• Ran the project's automated test suite (bench run-tests / unit tests) and the tests completed successfully.
• Executed a migration/install smoke path against a local test site to validate that DDL is skipped during install and executed during migrate, which succeeded.
• Verified linters/type checks and basic runtime flows for Party Master creation and index creation logging, all of which passed.

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