fix: dry-run correctness, verbose output gating, and CLI flag polish (v0.4.2)

[masonlet]

Changes

Continuation of #15 PR

Behavior changes

• Per-step output (Creating/Done/Finished...) now only prints under --verbose.
• Workspace clean no longer deletes node_modules for npm workspaces, too
  aggressive/unprompted. May return later behind an explicit flag.
• --clean was a silent no-op for npm projects; now warns under --verbose.

CLI changes

• Added --version.
• Short flags reshuffled: -v → --verbose, -b moved from --build-type
  to --build, -p added for --profile.
• Help output grouped under headings (Connection/Build/Mono-repo/Diagnostics);
  fixed --build doc comment not showing in --help.

Fixes

• build_project called with swapped build_path/source_path args in mono mode.
• Removed duplicate "Detecting build system" header.
• --no-dry-run conflicted with itself instead of --dry-run.
• Corrected stale --init-config/--profile-add references in help/error text.
• Mono dry-run with a forced --build-system wrote real config/wrap/watch
  files and spawned a real process instead of just reporting what would
  happen.
• Single-repo dry-run with a forced --build-system printed "Project
  finished" instead of "Would finish".
• Fixed a duplicate blank line before the final message in npm builds
  (--no-build, non-verbose), npm had no equivalent to cmake/meson's
  "Creating build directory" line to separate two independently-printed
  section breaks.

Internal

• Removed configure_and_build (folded into build_project).
• Flattened workspace path/mono_dir/build_dir into shared WorkspaceTarget.
• Extracted io_error_msg and detect_or_dry_run helpers.
• Generalized dry_run_or_do to take IoCtx/RunFlags instead of the full
  RunCtx, so it can be reused by config/wrap/watch generators that don't
  have a Runner.
• generate_watch_scripts returns bool so watch scripts only open when generated.
• Clarified run() # Errors doc.