fix: smart uninstaller cleanup + prevent nested .ragcode dirs

[doITmagic]

Description

Eliminates incomplete uninstallation caused by hardcoded directory guesses (~/Projects, ~/code, etc.). Replaces with a data-driven strategy that queries every authoritative source available on the system. Also fixes the root cause of nested .ragcode/ directories being created when IDEs open sub-directories.

Changes:

• internal/uninstall/uninstall.go — cleanup from 4 sources: registry, Qdrant file_path payloads, JetBrains/VSCode/AI-IDE configs (resolveIDEPaths), shallow $HOME scan
• internal/uninstall/uninstall_test.go — updated tests for orphan sibling detection
• pkg/workspace/detector/detector.go — removed .ragcode from workspace markers (prevented hijacking root detection)
• pkg/workspace/resolver/resolver.go — centralized applyNestedOverride to prevent split-indexing on sub-directory opens

Type of change

• Bug fix (non-breaking change which fixes an issue)

Checklist:

• I have performed a self-review of my own code
• I have formatted my code with go fmt ./...
• I have run tests go test ./... and they pass
• I have verified integration with Ollama/Qdrant (if applicable)
• I have updated the documentation accordingly

[Copilot]

Pull request overview

Improves uninstall completeness by replacing hardcoded directory guesses with data-driven discovery (registry, Qdrant payloads, IDE configs, shallow home scan) and reduces accidental creation of nested .ragcode/ directories by adjusting workspace detection/resolution.

Changes:

• Expand uninstall cleanup strategy to scan authoritative sources (registry + Qdrant + IDE configs + home shallow scan).
• Remove .ragcode as a workspace marker and centralize nested-workspace override logic in the resolver.
• Update uninstall tests and bump CLI version.

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
internal/uninstall/uninstall.go	New discovery-based scanning for orphaned .ragcode/ dirs; IDE/Qdrant-based root discovery.
internal/uninstall/uninstall_test.go	Updates expectations to reflect fallback scan cleanup.
pkg/workspace/detector/detector.go	Removes .ragcode from marker list to avoid workspace root “hijacking”.
pkg/workspace/resolver/resolver.go	Centralizes nested workspace override via applyNestedOverride.
cmd/rag-code-mcp/main.go	Version bump to 2.1.87.

Comments suppressed due to low confidence (1)

pkg/workspace/detector/detector.go:62

• Removing ".ragcode" from the marker list means detectFromMetadata() can now fail for workspaces that only have the managed .ragcode/root metadata (and no other markers like .git/go.mod). That makes previously indexable “markerless” folders undiscoverable and will return "metadata referenced root ... but no markers found". Consider treating the metadata file itself as sufficient, or adding a dedicated marker check for .ragcode/root without reintroducing .ragcode directory hijacking.

			"artisan",
			".agent",
			".idea",
			".vscode",
			".vs",
			".cursor",
			".windsurf",
			"AGENTS.md",
			"CLAUDE.md",
		},
		MaxDepth:         10,
		MetadataFileName: filepath.Join(".ragcode", "root"),
	}

[doITmagic]

Verified this and you're correct. Updated inspectDir to explicitly treat the .ragcode/root metadata file as a valid marker so markerless workspaces remain discoverable.

[doITmagic]

Fixed. Added curl timeouts in Qdrant fetches, corrected the off-by-one depth limit and the IDE data dir sentinel, and explicitly lowered Confidence/Reason when applying a nested workspace outline fallback.

[Copilot]

Pull request overview

Copilot reviewed 5 out of 5 changed files in this pull request and generated 2 comments.

[doITmagic]

Addressed the final two items: Gated the SkipDir return flag behind info.IsDir() so file walkers don't unnecessarily panic-abort when hitting deep configurations, and fully restored the IDE grandparent directory parsing to include both the configuration and umbrella projects directory.