docs: Fix documentation inaccuracies from review feedback

[Copilot]

Corrects 23 documentation inaccuracies identified in PR #9 review where examples and references diverged from actual implementation.

Configuration & Paths

• Config file location: ~/.claude/mnemonic/config.yaml → ~/.config/mnemonic/config.json (XDG-compliant)
• Config property: config.memory_root → config.memory_store_path
• Git repository location: Under project subdirectory → Memory store root
• Directory structure examples aligned with commands/setup.md behavior

Command Syntax

• /mnemonic:gc: Replaced non-existent flags (--older-than, --namespace) with actual (--dry-run, --archive, --compress)
• /mnemonic:custodian: Subcommands not flags (validate-links --fix not --validate-links --fix)
• /mnemonic:status: Removed non-existent "Ontology: loaded" line from expected output
• /mnemonic:validate: Corrected usage for ontology validation

API Documentation

• add_relationship() signature: (memory_path, rel_type, target_id, label) not (source_path, target_id, rel_type, label)
• get_inverse() example: Valid MIF type "supersedes" not invalid "depends_on"
• get_ontology_file(): Clarified returns bundled MIF base, not custom ontologies
• PathResolver.get_ontology_paths(): Excludes bundled base ontology
• Removed non-existent convenience functions from import examples

Relationship Types

Replaced invalid types with actual MIF spec types from lib/relationships.py:

- depends_on/dependency_of
- caused_by/causes  
- resolves/resolved_by
+ uses/UsedBy
+ created/Created
+ supersedes/SupersededBy
+ part_of/Contains
+ derived_from/Derives

Tutorial Content

• Removed broken links to 7 non-existent tutorial files
• Updated "Next Steps" to reference existing docs (cli-usage.md, ontologies.md, architecture.md)
• Adjusted learning path time estimates to reflect available content

Cleanup

• Removed MNEMONIC_DEBUG environment variable references (not implemented)
• Removed non-existent Makefile targets (make test-hooks, make test-lib)
• Updated debugging instructions to use command output capture instead

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[Copilot]

Pull request overview

This PR corrects documentation examples and references to better match Mnemonic’s current configuration locations, CLI syntax, and Python API signatures.

Changes:

• Align config/path references with XDG config (~/.config/mnemonic/config.json) and unified memory store layout.
• Update CLI examples for gc, custodian, and validate to reflect existing commands/flags.
• Fix API reference examples/signatures for relationships, ontology loading, and path helpers; remove references to non-existent tutorial files.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 6 comments.

File	Description
docs/tutorials/getting-started.md	Updates setup/status guidance and “Next steps” links to reflect current behavior and existing docs.
docs/tutorials/README.md	Removes links to non-existent tutorials and adjusts learning-path expectations accordingly.
docs/troubleshooting.md	Updates config path references and CLI examples for validation, GC, custodian, and debugging guidance.
docs/api-reference.md	Corrects multiple API examples/signatures and clarifies ontology/path resolution behavior.

[Copilot]

In this import list you switched to get_all_memory_roots_with_legacy and removed get_memory_path, but the code block below still calls get_memory_path(...) and get_all_memory_roots(). Since lib.paths does not expose convenience functions for those names, the example is now copy/paste-broken; update the snippet to use PathResolver.get_memory_path(...) and get_all_memory_roots_with_legacy() (or add/document the missing convenience wrappers).

[Copilot]

The setup command does not write organization/project into ~/.config/mnemonic/config.json (it only stores version and memory_store_path), and it also doesn’t initialize a default ontology.yaml or any index structures. Please adjust these bullets to match /mnemonic:setup (commands/setup.md) behavior.

[Copilot]

Step 4 hardcodes the default ~/.claude/mnemonic/... path. Since /mnemonic:setup allows configuring memory_store_path, consider showing how to derive the path from ~/.config/mnemonic/config.json (or reference $STORE_PATH_EXPANDED/get_memory_root()), otherwise the verification step will be wrong for non-default setups.

[Copilot]

The /mnemonic:status example output here doesn’t match the current /mnemonic:status command output format (commands/status.md prints sections like "=== Mnemonic Status ===" and doesn’t output these checkmark lines). Consider updating this example to reflect the actual output, or point readers at the sections/fields to look for instead of a literal block.

[Copilot]

The description for the Architecture link is misleading: docs/architecture.md explains Mnemonic’s design and components, not how to “Create a comprehensive project knowledge base”. Update the link description to reflect the content (e.g., understanding how Mnemonic works).

Suggested change

	3. **[Architecture](../architecture.md)** - Create a comprehensive project knowledge base
	3. **[Architecture](../architecture.md)** - Understand Mnemonic’s architecture and components

[Copilot]

These ontology validation commands reference .claude/mnemonic/ontology.yaml, which only exists under the legacy scheme. With the unified store, project ontologies live under the configured memory store (e.g. ~/.claude/mnemonic/{org}/{project}/ontology.yaml), and /mnemonic:setup doesn’t create an ontology file by default. Update this section to reflect the correct file location(s) and/or how to find them via config + org/project.