docs: replace deprecated --ai flag with --integration in all documentation (#2359)

* docs: replace deprecated --ai flag with --integration in all documentation

Replace all user-facing --ai, --ai-skills, and --ai-commands-dir references
with their modern equivalents:

- --ai <agent> → --integration <agent>
- --ai-skills → --integration-options="--skills"
- --ai-commands-dir <dir> → --integration generic --integration-options="--commands-dir <dir>"

Updated files:
- README.md (~17 occurrences)
- docs/installation.md (~8 occurrences)
- docs/upgrade.md (~11 occurrences)
- docs/local-development.md (~5 occurrences)
- CONTRIBUTING.md (1 occurrence)
- extensions/EXTENSION-USER-GUIDE.md (1 occurrence)
- src/specify_cli/__init__.py (docstring examples and error messages)

Left unchanged:
- CHANGELOG.md (historical record)
- Test files (intentionally exercise deprecated flag path)
- CLI flag implementation (backward compatibility)

Closes #2358

* docs: address review feedback on pre-existing issues

- Fix duplicate copilot example in README.md (replace with codex)
- Fix invalid gemini --integration-options="--skills" example (gemini
  does not support --skills)
- Update generic integration comment from 'Unsupported agent' to
  'Bring your own agent; requires --commands-dir'
- Clarify EXTENSION-USER-GUIDE.md: skills auto-register for
  skills-based integrations, not only with --integration-options

* docs: replace bare 'AI agent' / 'AI assistant' with 'coding agent' throughout

Full sweep across all documentation and user-facing CLI messages to
align terminology. Bare references like 'AI agent', 'AI assistant',
and 'AI Agent' are replaced with 'coding agent' or 'coding agent
integration' as appropriate.

Intentionally left unchanged:
- 'AI coding agent' (already correct expanded form)
- Deprecated --ai flag help text and error messages (describes the
  deprecated flag itself)
- Community extension descriptions (external project text)
- 'generated by an AI' in CONTRIBUTING.md (general AI, not agent)

* docs: address review — remove deprecated --offline, qualify --skills scope

- Remove --offline from docstring examples (deprecated no-op)
- Remove --offline from CONTRIBUTING.md testing example
- Replace --offline instructions in docs/installation.md with note that
  bundled assets are used by default
- Qualify --integration-options="--skills" in README.md to note it only
  applies to integrations that support skills mode

docs/local-development.md

@@ -20,7 +20,7 @@ You can execute the CLI via the module entrypoint without installing anything:
 ```bash
 # From repo root
 python -m src.specify_cli --help
-python -m src.specify_cli init demo-project --ai claude --ignore-agent-tools --script sh
+python -m src.specify_cli init demo-project --integration claude --ignore-agent-tools --script sh
 ```
 
 If you prefer invoking the script file style (uses shebang):
@@ -52,7 +52,7 @@ Re-running after code edits requires no reinstall because of editable mode.
 `uvx` can run from a local path (or a Git ref) to simulate user flows:
 
 ```bash
-uvx --from . specify init demo-uvx --ai copilot --ignore-agent-tools --script sh
+uvx --from . specify init demo-uvx --integration copilot --ignore-agent-tools --script sh
 ```
 
 You can also point uvx at a specific branch without merging:
@@ -69,14 +69,14 @@ If you're in another directory, use an absolute path instead of `.`:
 
 ```bash
 uvx --from /mnt/c/GitHub/spec-kit specify --help
-uvx --from /mnt/c/GitHub/spec-kit specify init demo-anywhere --ai copilot --ignore-agent-tools --script sh
+uvx --from /mnt/c/GitHub/spec-kit specify init demo-anywhere --integration copilot --ignore-agent-tools --script sh
 ```
 
 Set an environment variable for convenience:
 
 ```bash
 export SPEC_KIT_SRC=/mnt/c/GitHub/spec-kit
-uvx --from "$SPEC_KIT_SRC" specify init demo-env --ai copilot --ignore-agent-tools --script ps
+uvx --from "$SPEC_KIT_SRC" specify init demo-env --integration copilot --ignore-agent-tools --script ps
 ```
 
 (Optional) Define a shell function:
@@ -123,7 +123,7 @@ When testing `init --here` in a dirty directory, create a temp workspace:
 
 ```bash
 mkdir /tmp/spec-test && cd /tmp/spec-test
-python -m src.specify_cli init --here --ai claude --ignore-agent-tools --script sh  # if repo copied here
+python -m src.specify_cli init --here --integration claude --ignore-agent-tools --script sh  # if repo copied here
 ```
 
 Or copy only the modified CLI portion if you want a lighter sandbox.