Restructure: single source of truth + library-first analysis

[dschneidinger]

Establish run.yaml as the single source of run parameters and route OSIRIS plotting/shock-fitting through pyVisOS, eliminating config duplication across runme scripts, run_manifest.yaml, and analysis configs.

Run spec (Phases 1-2):

• FLASH_OSIRIS_define.py gains --config <run.yaml>; freezes the resolved spec to <sim_dir>/run.yaml and trims run_manifest.yaml to provenance + derived.
• runs/.run.yaml: structured single source per run; runme_.sh reduced to thin --config wrappers. Template emits indexed nx_p(1:1) so osiris_utils can parse 1D decks.
• src/run_spec.py: RunSpec.from_sim_dir resolves run.yaml -> run_manifest (cli_command) -> runme*.sh; re-exported from analysis_utils. Deleted the brittle parse_runme/load_runme/find_runme/input_deck helpers.
• config/*.yaml stripped to derived-from-data annotations only (sim_dir, shock fit, dump_params, flash seeds).

Analysis (Phases 3-5):

• src/shock.py single-sources front detection (detect_front_edge for OSIRIS, detect_front_gradient for FLASH) and robust_linfit (sigma-clipping fit). overview.py and flash_overview.py both use it; flash_utils.detect_front delegates to it.
• OSIRIS plotting defaults to osh5vis (osimshow/osplot1d/ossemilogy) with labels/units sourced from H5Data data_attrs; loading stays on osh5io + path helpers + StreakBuilder. overview.py and convergence_scan.py migrated.

Tests: src/run_spec and src/shock unit tests (82 pytest pass); CI deps updated.