Summary

Removes the 32 deprecated CLI aliases retained for one version after PR #195's 78→12 consolidation.

Aliases removed: affected, arch-metrics, architecture, binary-scan, circular, complexity, dashboard, dataflow, dead-code, dependents, diff, env-check, git-status, graph-schema, import-snapshot, init, lsp-status, orient, outline, ownership, perf-hint, query-graph, regex-audit, secrets, semantic-query, side-effect, smell, staleness, symbols, taint, trace, vuln-scan.

What changed

• Removed register_command() calls from 30 alias modules in scripts/commands/. The modules themselves are kept because the 12 umbrella commands import them via importlib for their --check sub-analyses (e.g. audit.py imports commands.dead_code, security.py imports commands.secrets).
• Deleted 2 alias modules that no umbrella imports: symbols.py, semantic_query.py (semantic search is reached via search --mode semantic).
• Removed deprecated_alias_for parameter from register_command() and the deprecation-warning dispatch block in codelens.py.
• Updated README deprecated aliases section.
• Updated tests that exclusively tested deprecated-alias behavior.

Supporting fixes (required to keep umbrella + MCP surface working after alias removal)

MCP server dispatch fallback (scripts/mcp_server.py)

Added an importlib fallback in _execute_command() so MCP tools that dispatch to the now-unregistered alias modules (codelens_architecture, codelens_secrets, codelens_symbols, codelens_trace, etc.) keep working. The CLI alias is gone (argparse rejects with invalid choice), but the MCP surface is preserved.

--diff-base post-filter (scripts/codelens.py)

Extended the post-filter to handle umbrella commands. The old logic checked args.command against alias names; now it also recognizes the umbrella names (security, audit, impact, context, deps) and filters each sub-result in result['r'] individually, attaching the diff_scope summary at the top level.

--deep hybrid analysis (scripts/codelens.py)

Extended --deep post-processing to handle audit --check <category> by mapping the check name back to the alias name (smell, dead-code, complexity) and targeting the enhancement at the matching sub-result in result['r'].

Definition of Done verification

• Semua 32 file alias .py dihapus dari scripts/commands/ — partial: 2 files deleted (symbols.py, semantic_query.py); 30 files kept as implementation modules (umbrellas import them via importlib). See Findings below.
• codelens --help tidak menampilkan alias manapun — only the 12 umbrella commands appear.
• Memanggil alias lama menghasilkan invalid choice (verified for dead-code, secrets, symbols).
• codelens --command-count tetap return 12.
• README deprecated aliases section diupdate.

Test results

Baseline (at 7fa4096): 22 pre-existing failures (test_doctor, test_search_pagination, test_confidence, etc. — environment / pre-existing).
This PR: 18 failures — 0 new regressions, 4 pre-existing failures fixed:

• test_cli.py::TestArgparseFormatConflictRegression::test_affected_with_filter_short_does_not_crash
• test_cli.py::TestArgparseFormatConflictRegression::test_no_duplicate_f_in_subparsers
• test_compact_format.py::TestMCPGraphSchemaTool::test_graph_schema_tool_present
• test_compact_format.py::TestMCPGraphSchemaTool::test_graph_schema_tool_has_workspace_param

Pre-existing failures ignored per CONTEXT.md: test_integration.py (worktree path arithmetic), test_lsp_server.py (lsprotocol optional dep), test_large_file_parsing.py (tree-sitter segfault).

Findings (out of scope, flagged for BOS)

DoD #1 says "delete all 32 .py files". This is impossible without breaking the 12 umbrella commands, which import these modules via importlib for their --check sub-analyses. For example, audit.py does importlib.import_module('commands.dead_code') to run the dead-code sub-analysis. Deleting dead_code.py would break codelens audit --check dead-code.

The approach taken here (remove the registration, keep the module) achieves all user-facing DoD items (#2, #3, #4, #5) while preserving the implementation. The 2 modules that no umbrella imports (symbols.py, semantic_query.py) were deleted entirely.

Closes #199.