Extract agent context updates into bundled agent-context extension

[Copilot]

New Feature

Coding agent context file management (<!-- SPECKIT START --> / <!-- SPECKIT END --> injection into CLAUDE.md, .github/copilot-instructions.md, etc.) was hardcoded into IntegrationBase, with no way to opt out or customize markers. This change moves that behavior into a bundled agent-context extension driven by .specify/extensions/agent-context/agent-context-config.yml.

What does this feature do?

Adds extensions/agent-context/ (bundled: true, opt-out) that owns the lifecycle of the managed context section. Both the Python paths and the new shell/PowerShell scripts read context_file and context_markers from .specify/extensions/agent-context/agent-context-config.yml — single source of truth, no per-agent logic, user-customizable markers.

# .specify/extensions/agent-context/agent-context-config.yml
context_file: CLAUDE.md
context_markers:
  start: "<!-- SPECKIT START -->"
  end: "<!-- SPECKIT END -->"

Implementation details

• integrations/base.py

  • _resolve_context_markers(project_root) — reads context_markers from agent-context-config.yml, falls back to CONTEXT_MARKER_START / CONTEXT_MARKER_END constants per side.
  • _agent_context_extension_enabled(project_root) — reads .specify/extensions/.registry; returns True when registry/entry absent (backwards compat) or enabled is not literally False.
  • upsert_context_section() / remove_context_section() now use the resolved markers and short-circuit when the extension is disabled. upsert_context_section() emits a deprecation warning (v0.12.0) since inline context updates are being replaced by the extension.

• specify_cli/commands/init.py

  • specify init writes context_file to the agent-context extension config (not init-options.json).
  • Auto-installs the bundled agent-context extension during specify init (after init-options.json is saved, so skill registration works).
  • ensure_executable_scripts runs after extension install so extension scripts get execute bits.

• specify_cli/__init__.py

  • _update_init_options_for_integration() writes context_file to the extension config, preserving user-customized markers.
  • _clear_init_options_for_integration() clears context_file in the extension config and removes legacy keys from init-options.json.
  • _load_agent_context_config() / _save_agent_context_config() — helpers for reading/writing the extension config.

• extensions/agent-context/ — extension.yml (id agent-context, hooks after_specify / after_plan), README.md, commands/speckit.agent-context.update.md, and bash + PowerShell update-agent-context scripts. Both scripts parse agent-context-config.yml, resolve markers (with default fallback), auto-detect the most recent specs/*/plan.md when no plan path is supplied, and perform the same upsert algorithm as the Python path (CRLF normalization, BOM strip, marker-corruption recovery). Scripts include path traversal guards rejecting absolute paths and .. segments.

• extensions/catalog.json — agent-context registered as bundled: true, alphabetized first.

• AGENTS.md — wrapper-script and dispatcher-script guidance removed; replaced with the agent-context-config.yml flow and the specify extension disable agent-context opt-out.

• Command templates — All 8 non-constitution commands (specify, clarify, plan, tasks, checklist, implement, analyze, taskstoissues) now include a directive to load /memory/constitution.md for project principles and governance constraints.

• tests/extensions/test_extension_agent_context.py — 34 tests covering extension layout, catalog entry, marker resolution (defaults / custom / partial / invalid / corrupt YAML), upsert+remove with custom markers, the disabled-extension gate (upsert returns None, remove returns False and leaves file untouched), deprecation warning output, and extension config writers.

• tests/integrations/test_integration_generic.py — Parametrized test verifying all 8 commands reference constitution.md.

Backwards compatibility

• Missing agent-context-config.yml or missing context_markers → class-constant defaults, identical to current behavior.
• Legacy context_file in init-options.json → agents.py falls back to reading it when extension config is absent.
• Missing extension registry or missing agent-context entry → treated as enabled, so existing projects continue to receive context updates without re-init.
• All 30+ existing integrations are unchanged; markers remain defined only on IntegrationBase.

[Copilot]

Pull request overview

This PR refactors agent-context-file management (the <!-- SPECKIT START --> / <!-- SPECKIT END --> block injected into files like CLAUDE.md) out of IntegrationBase and into a new bundled agent-context extension. Configuration now flows through .specify/init-options.json (context_file, context_markers), giving users opt-out (specify extension disable agent-context) and customizable markers, with parallel bash/PowerShell scripts that mirror the Python upsert logic.

Changes:

• Adds a bundled agent-context extension (manifest, README, command, bash + PowerShell scripts) and registers it in extensions/catalog.json.
• Extends IntegrationBase with _resolve_context_markers() and _agent_context_extension_enabled(), gating both upsert_context_section() and remove_context_section() on the registry, and seeds/clears context_markers in init-options.json from specify_cli.__init__.
• Updates AGENTS.md and adds 25 tests covering layout, marker resolution, custom-marker upsert/remove, the disabled-gate, and init-options writers.

Show a summary per file

File	Description
src/specify_cli/integrations/base.py	New marker-resolution + extension-enabled helpers; upsert/remove use them.
src/specify_cli/__init__.py	New tracker step that auto-installs bundled agent-context; seeds/clears context_markers.
extensions/catalog.json	Registers agent-context as bundled: true.
extensions/agent-context/extension.yml	Extension manifest with after_specify / after_plan hooks.
extensions/agent-context/README.md	User-facing docs for opt-out and configuration.
extensions/agent-context/commands/speckit.agent-context.update.md	Slash-command spec referencing the bash/ps1 scripts.
extensions/agent-context/scripts/bash/update-agent-context.sh	Bash hook that re-renders the managed section.
extensions/agent-context/scripts/powershell/update-agent-context.ps1	PowerShell counterpart.
AGENTS.md	Removes wrapper-script guidance; documents the new init-options.json flow and opt-out.
tests/extensions/test_extension_agent_context.py	25 new tests for the extension and plumbing.

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