Summary

• Adds step 2 to putup configure: automatically copy subdir tup.config files from the config root to the build tree for out-of-tree builds
• Enables per-component scoped configs (e.g., gmp/tup.config, mpfr/tup.config) to work seamlessly with out-of-tree variant builds
• Removes false-positive variant detection that skipped directories containing both a Tupfile and a tup.config

Three-step configure flow

putup configure [--config X] [-B build]:
  Step 1: Install root config            (only if --config)
  Step 2: Copy source subdir tup.config  (always; no-op if in-tree)
  Step 3: Run config-generating rules    (always; no-op if none exist)

Step 2 walks the config root, finds subdir tup.config files, and copies them to corresponding locations in the build tree. This handles the gap where --config only installed the root config but subdir scoped configs had no mechanism to reach the build tree.

Changes

• src/cli/cmd_configure.cpp — New install_source_configs helper; refactored configure_single_variant into unified three-step flow with single discover_layout call
• src/cli/context.cpp — Removed variant-directory skip from discover_tupfile_dirs (directories with both Tupfile and tup.config are valid for scoped configs)
• test/unit/test_e2e.cpp — 4 new E2E scenarios covering subdir config copy, scoped merge integration, in-tree no-op, and mixed static + auto-gen configs
• docs/reference.md — Updated §3.5 configure flow documentation and CLI option descriptions

Test plan

• All 335 existing tests pass (including 30 variant tests)
• New test: configure copies subdir configs to build tree
• New test: configure + subdir configs + build uses scoped merge
• New test: configure skips copy for in-tree builds
• New test: mixed static + auto-gen config handling

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