feat(extensions,presets): add priority-based resolution ordering

[mbachorik]

Summary

• Add priority-based resolution ordering for extensions and presets
• Lower priority number = higher precedence (default: 10)
• Backwards compatible with existing installations

Changes

Extensions

• Add list_by_priority() method to ExtensionRegistry
• Add --priority option to extension add command
• Add extension set-priority command
• Show priority in extension list and extension info
• Preserve priority during extension update
• Update RFC documentation

Presets

• Add preset set-priority command
• Show priority in preset info output
• Use priority ordering in PresetResolver for extensions

Test plan

• 325 tests passing
• Linter clean
• Manual testing with real extensions (jira, linear, reverse-eng)
• Manual testing with presets (priority resolution verified)
• Backwards compatibility verified (legacy entries default to priority 10)

Closes #1845
Closes #1854

🤖 Generated with Claude Code

[Copilot]

Pull request overview

Adds a priority field to extensions (and extends preset support) so resolution can be ordered deterministically, with lower numbers taking precedence, and exposes this via CLI commands and outputs.

Changes:

• Add priority-aware ordering to ExtensionRegistry and use it in preset template resolution for extensions.
• Add CLI support for setting priority (extension add --priority, extension set-priority, preset set-priority) and display priority in list/info.
• Add tests for priority behavior and backwards compatibility defaults (priority=10).

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
src/specify_cli/extensions.py	Adds priority persistence and ExtensionRegistry.list_by_priority() for ordering.
src/specify_cli/presets.py	Uses extension registry priority ordering during extension template resolution; adds preset registry update helper.
src/specify_cli/__init__.py	Adds CLI options/commands to set/display priority for extensions and presets; preserves priority on extension update.
tests/test_extensions.py	Adds unit + CLI tests for extension priority ordering, persistence, and legacy defaults.
tests/test_presets.py	Updates resolution tests to register extensions in registry; adds preset set-priority + legacy priority tests.
extensions/RFC-EXTENSION-SYSTEM.md	Documents the new priority field and CLI behaviors.

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[Copilot]

Pull request overview

Adds a priority-based ordering model (lower number = higher precedence, default 10) across extensions and presets to make template/command resolution deterministic, with CLI support to view and modify priority and tests/docs updates.

Changes:

• Introduces priority metadata and list_by_priority() for extensions (and enhances preset sorting determinism/back-compat).
• Adds CLI support for setting/displaying priority (extension add --priority, extension set-priority, preset set-priority, priority shown in info/list).
• Updates preset template resolution to iterate extensions by registry priority rather than directory name order; expands tests and RFC docs accordingly.

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
src/specify_cli/extensions.py	Adds extension list_by_priority() and persists priority during install/listing.
src/specify_cli/presets.py	Adds preset registry update(), strengthens list_by_priority() ordering, and resolves extension templates by extension priority.
src/specify_cli/__init__.py	Adds/updates CLI commands and output to set/show priority; preserves priority on extension update.
tests/test_extensions.py	Adds coverage for extension priority ordering, CLI integration, and legacy/back-compat behavior.
tests/test_presets.py	Updates resolver tests for new extension source attribution and adds tests for preset set-priority + legacy priority behavior.
extensions/RFC-EXTENSION-SYSTEM.md	Documents the new priority field, CLI flags/commands, and updated list output examples.

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[Copilot]

Pull request overview

Adds priority-based ordering to extension and preset resolution to make overrides deterministic across installs, aligning extension behavior with the existing preset priority model and exposing priority controls via the CLI.

Changes:

• Introduces priority support for extensions (registry sorting + install/add/update preservation + CLI display/commands).
• Extends preset tooling with preset set-priority, priority display in preset info, and backwards-compatibility handling for legacy entries.
• Updates template resolution to iterate extensions/presets by priority (lower number = higher precedence) and updates RFC docs/tests accordingly.

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
src/specify_cli/extensions.py	Adds priority-aware sorting (list_by_priority) and persists/returns priority during installs and listing.
src/specify_cli/presets.py	Adds registry update helper, makes preset ordering deterministic, validates priority on install, and resolves extension templates via registry priority order.
src/specify_cli/__init__.py	Adds/validates --priority for extension add, adds extension set-priority and preset set-priority, and displays priority in list/info outputs.
tests/test_extensions.py	Adds coverage for extension priority ordering, CLI integration, and legacy/compat behavior.
tests/test_presets.py	Updates resolver tests to register extensions in the registry and adds tests for preset set-priority + legacy preset behavior.
extensions/RFC-EXTENSION-SYSTEM.md	Documents the new priority field and CLI options/commands.

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