Expand specification with detailed code-derived behavior

[tkilias]

Motivation

• The existing specification was too high-level and did not reflect current runtime behavior observed in the CLI, installation orchestration, search resolution, and model validation code.
• The intent is to capture precise Given-When-Then scenarios derived from the implementation so docs and tests remain aligned.

Description

• Added a comprehensive doc/specification.rst that enumerates CLI requirements, orchestration flow, phase ordering, installer dispatch semantics (apt, apt repos, tools, pip, conda, R, micromamba, bazel), search/cache resolution rules, package-file validation constraints, history persistence, and YAML serialization behavior.
• Updated doc/index.rst to include a Specification entry so the new spec is part of the documentation TOC.
• The spec text documents concrete behaviors such as apt repo-before-package handling, pip URL rendering (<name> @ <url>), ephemeral build-tools for pip phases, conda channel/packaging aggregation, micromamba path semantics, and history serialization as single-build-step PackageFile YAMLs.

Testing

• Ran unit tests: pytest -q test/unit/pkg_mgmt/test_install_packages.py test/unit/model/test_model_validation.py test/unit/pkg_mgmt/search/test_find_binary.py test/unit/pkg_mgmt/search/test_find_variable.py and they all passed.
• Full test run produced 127 passed for the selected test suites.

---

Codex Task

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud