Consolidate repository tools and flatten Runtime sources

[zhoubot]

Repository maintenance commands were split across flows/scripts, flows/tools and tools, while Runtime implementation files sat beneath an unnecessary simulator/gfsim wrapper. Consolidate all maintenance entrypoints in tools/ and move compiled Runtime sources to runtime/.

Update CMake, build-tree archive lookups, Bash/Python/PowerShell root discovery, CI, tests and navigation together. Keep the Python package, C++ namespaces, installed headers, Runtime target and archive names unchanged. All four Runtime files are byte-identical renames; the logo and six badges remain unchanged. The earlier Python wrapper cleanup remains in #276 (python/pycircuit/src/pycircuit → python/pycircuit).

The moved retirement scanner now excludes its own rejection-pattern definitions while continuing to scan every neighboring tool. Its stale static-export expectation is corrected to match the existing public initializer. Independent regression tests reject prohibited neighboring helpers and missing/retired-added exports. Remove the obsolete test requiring tooling to occupy two separate roots.

Validation on this checkout:

• CompilerDev reconfigure, build and clean-prefix install passed; API gate 22/22.
• Python tests: 583 passed, 5 skipped (platform/dependency availability).
• Runtime-only build, installation, relocation and external consumer without LLVM passed.
• Strict MkDocs, changed-file pre-commit, governance, API hygiene, install retirement scan, shell syntax and active stale-path checks passed.
• 158 protected namespace/header/branding/contract/oracle/snapshot files remain byte-identical. Historical provenance remains intact; the oracle guide's current nightly command uses the new path.

Windows execution, full nightly and full example coverage were not run. The preview generator's pre-existing Runtime-header path assumption remains separate follow-up work; this change does not claim preview execution. Initial missing-tool environment failures and corrected passing results are retained under ignored docs/gates/logs/hierarchy-20261010/. No intermediate logs are committed.

[zhoubot]

Final candidate daeb0df342d1d7c74c8f32722083af7e8f7647ef has independent code-review APPROVE (no regression findings) and architecture CLEAR. The architecture review's final active oracle-guide command correction is included in this commit. Implementation and independent scanner tests/review used separate instances; review evidence remains in ignored local logs.

Both required GitHub checks passed on this exact head. Local evidence: Python 583 passed/5 skipped; API 22/22; Runtime-only install/relocation/consumer 1/1; scanner tests 15/15; strict docs, pre-commit and repository checks passed. Public namespaces, installed Runtime contracts, logo and badges are preserved. Existing preview gap is recorded in #272. Windows and full nightly remain unclaimed.