Fix init-force-preset-desync: reapply presets/extensions on init --here --force (#3995)

Apply the remediation from the bug assessment on issue #3990.

After integration setup() and manifest.save(), when --force is used
(re-initializing an existing project), call _register_presets_for_agent
and _register_extensions_for_agent so that previously-installed presets
and extensions are recomposed on top of the freshly-regenerated core
files. Without this, preset-composed files reverted to pure core while
the preset registry continued to report them as installed.

This mirrors the same pattern already present in integration_upgrade()
(added in PR #3853 / issue #3849 for the upgrade path).

Refs #3990

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Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

src/specify_cli/commands/init.py

@@ -635,6 +635,30 @@ def register(app: typer.Typer) -> None:
                 )
                 manifest.save()
 
+                if force:
+                    from ..integrations._helpers import (
+                        _register_extensions_for_agent,
+                        _register_presets_for_agent,
+                    )
+
+                    _register_extensions_for_agent(
+                        project_path,
+                        resolved_integration.key,
+                        force=True,
+                        continuing=(
+                            "The project was re-initialized, but installed extensions"
+                            " may need re-registration."
+                        ),
+                    )
+                    _register_presets_for_agent(
+                        project_path,
+                        resolved_integration.key,
+                        continuing=(
+                            "The project was re-initialized, but installed presets"
+                            " may need re-registration."
+                        ),
+                    )
+
                 integration_settings = _with_integration_setting(
                     {},
                     resolved_integration.key,