Replace shell-based context updates with marker-based upsert

Replace ~3500 lines of bash/PowerShell agent context update scripts
with a Python-based approach using <!-- SPECKIT START/END --> markers.

IntegrationBase now manages the agent context file directly:
- upsert_context_section(): creates or updates the marked section at
  init/install/switch time with a directive to read the current plan
- remove_context_section(): removes the section at uninstall, deleting
  the file only if it becomes empty
- __CONTEXT_FILE__ placeholder in command templates is resolved per
  integration so the plan command references the correct agent file
- context_file is persisted in init-options.json for extension access

The plan command template instructs the LLM to update the plan
reference between the markers in the agent context file.

Removed:
- scripts/bash/update-agent-context.sh (857 lines)
- scripts/powershell/update-agent-context.ps1 (515 lines)
- 56 integration wrapper scripts (update-context.sh/.ps1)
- templates/agent-file-template.md
- agent_scripts frontmatter key and {AGENT_SCRIPT} replacement logic
- update-context reference from integration.json
- tests/test_cursor_frontmatter.py (tested deleted scripts)

Added:
- upsert/remove context section methods on IntegrationBase
- __CONTEXT_FILE__ placeholder support in process_template()
- context_file field in init-options.json (init/switch/uninstall)
- Per-integration tests: context file correctness, plan reference,
  init-options persistence (78 new context_file tests)
- End-to-end CLI validation across all 28 integrations

Author: mnriem

pyproject.toml

@@ -28,7 +28,6 @@ packages = ["src/specify_cli"]
 [tool.hatch.build.targets.wheel.force-include]
 # Bundle core assets so `specify init` works without network access (air-gapped / enterprise)
 # Page templates (exclude commands/ — bundled separately below to avoid duplication)
-"templates/agent-file-template.md" = "specify_cli/core_pack/templates/agent-file-template.md"
 "templates/checklist-template.md" = "specify_cli/core_pack/templates/checklist-template.md"
 "templates/constitution-template.md" = "specify_cli/core_pack/templates/constitution-template.md"
 "templates/plan-template.md" = "specify_cli/core_pack/templates/plan-template.md"