Extract agent context updates into bundled agent-context extension (#2546)

* Initial plan

* Extract agent context updates into bundled agent-context extension

* Potential fix for pull request finding 'Unused import'

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* Potential fix for pull request finding 'Unused import'

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* fix: address review comments on agent-context extension

- bash: parse init-options.json with a single python3 invocation instead
  of three separate read_json_field calls, for parity with the PowerShell
  ConvertFrom-Json approach and to avoid divergent error semantics
- bash: use parameter expansion to strip PROJECT_ROOT prefix from plan
  path instead of sed interpolation, avoiding special-character fragility
- powershell: limit Get-ChildItem to -Depth 1 so plan.md discovery matches
  the bash glob specs/*/plan.md (one level deep) — fixes cross-platform
  inconsistency with nested plan.md files
- powershell: replace Substring+Length relative-path with
  [System.IO.Path]::GetRelativePath for robustness across case/PSDrive
  differences
- __init__.py: move agent-context extension install to after
  save_init_options so init-options.json is present when hooks run
- __init__.py: seed context_markers in init-options only when
  context_file is truthy; avoids noise for integrations without a context
  file
- integrations/base.py: narrow blanket except Exception in
  _resolve_context_markers to ImportError / (OSError, ValueError) so
  unexpected bugs surface instead of being silently swallowed

* fix: gate context_markers in _update_init_options_for_integration on context_file

Apply the same gating logic used during `specify init`: only write
context_markers to init-options.json when the integration actually has a
context_file set.  When switching to an integration without a context file
the stale markers are removed, keeping the two init paths consistent.

* fix: move context_file/context_markers from init-options.json to agent-context extension config

* Potential fix for pull request finding 'Unused global variable'

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* fix: clarify local import comment in agents.py

* Fix remaining agent-context review findings

* Fix follow-up agent-context review issues

* Address review feedback: narrow except, improve PyYAML messaging, surface config-written note

* Fix double-space in PyYAML install hint message

* Potential fix for pull request finding 'Empty except'

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* Potential fix for pull request finding 'Empty except'

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* Address latest agent-context review feedback

* Harden bash config parse output handling

* Clarify ImportError-only fallback comment

* Apply review feedback: drop dead try/except, guard ext-config creation, explicit ConvertFrom-Yaml check

* Remove redundant $Options = $null in PS1 catch block

* Add constitution directives, deprecation warning, agent-context auto-install, and init flow fix

- Add constitution-loading directive to specify, clarify, tasks, checklist, taskstoissues commands
- Add deprecation warning (v0.12.0) in upsert_context_section()
- Auto-install agent-context extension during specify init
- Move context_file from init-options.json to agent-context extension config
- Add tests: deprecation warning, corrupt config, constitution directives
- Update file inventories across all integration tests

* Address review: fix init ordering, test coverage, and hermes inventory

- Move agent-context extension install after init-options.json is saved
  so skill registration can read ai_skills + integration key
- Write extension config after install (avoids template overwriting context_file)
- Fix test_defaults_when_markers_field_missing to truly test missing markers key
- Update hermes tests to allow extension-installed agent-context skill

* Address review: chmod ordering, preserve markers, PS1 Python check, YAML key order

- Move ensure_executable_scripts after agent-context extension install
  so extension scripts get execute bits set
- Use preserve_markers=True on reinit to keep user-customized markers
- Add Python 3 version check in PowerShell fallback (matching bash behavior)
- Add sort_keys=False to yaml.safe_dump for stable config output

* Address review: path traversal guards and docstring fix

- Reject absolute paths and '..' segments in context_file in both bash and
  PowerShell scripts to prevent writes outside the project root
- Fix docstring in _update_init_options_for_integration to accurately
  describe marker preservation behavior

* Address review: strict enabled check, docstring, segment-level path traversal

- Use 'is not False' for enabled check so only literal False disables
- Update upsert_context_section docstring to mention disabled-extension return
- Fix path traversal guards to check actual path segments, not substrings
  (allows filenames like 'notes..md' while rejecting '../' traversal)

* Address review: UnicodeError handling, missing extension warning

- Add UnicodeError to exception tuples in _load_agent_context_config and
  _resolve_context_markers so garbled UTF-8 config files fall back to defaults
- Emit error (with reinstall command) instead of silent skip when bundled
  agent-context extension is not found during init

* Address review: bash backslash traversal guard, wheel packaging

- Reject backslash separators and Windows drive-letter paths in bash
  context_file validation (prevents traversal on Git-Bash/Windows)
- Add extensions/agent-context to pyproject.toml force-include so the
  bundled extension is included in wheel builds

* Address review: write extension config before init-options.json

- Reorder writes in _update_init_options_for_integration so the
  agent-context extension config is updated first; if it fails,
  init-options.json remains consistent with the previous state

---------

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Co-authored-by: Manfred Riem <15701806+mnriem@users.noreply.github.com>
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