「debugging」の検索結果

Use when a decision needs deep multi-source technical research with cited evidence — technology evaluation, ecosystem comparison, standards/spec fact-finding, "how do others solve X". Triggers on "research X", "deep dive on X", "evaluate X vs Y", "find best practices for X". NOT for library/API doc lookup (see mk:docs-finder); NOT for one-shot URL fetch (see mk:web-to-markdown); NOT for internal codebase discovery (see mk:scout); NOT for project-only Q&A (see mk:ask-me); NOT for comparing solution designs (see mk:brainstorming); NOT for root-cause debugging (see mk:investigate); NOT for wiki ingestion of sources (see mk:wiki-research).

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Use when a problem requires structured step-by-step reasoning before acting. Prevents jumping to conclusions or guessing root causes without evidence. Triggers on complex debugging, multi-step analysis, hypothesis verification, or when mk:fix invokes diagnosis phase. NOT for being stuck on approach (too many implementations, forced assumptions, innovation block) — use mk:problem-solving instead.

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Fast parallel codebase scouting. Spawns multiple Explore subagents to search directories simultaneously, returning a consolidated file map with architecture fingerprint, complexity estimates, and routing suggestions. Use before planning, debugging, or any task spanning multiple directories. NOT for reading a single known file in depth (use Read directly); NOT for semantic find-usages or go-to-definition.

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Resolve an in-progress git merge or rebase conflict end to end: read the conflict state, recover each side's original intent, resolve every hunk, run the project's checks, and prepare the merge/rebase for an explicitly approved finish. Use when asked to "resolve merge conflicts", "fix this rebase", "finish the merge", or when `git status` shows conflicted (unmerged) paths. NOT for the full ship pipeline that merges the base branch first (see mk:ship); NOT for debugging a runtime bug or test failure unrelated to a conflict (see mk:investigate / mk:fix).

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Session-scoped safety guardrails for destructive commands. Warns before rm -rf, DROP TABLE, force-push, git reset --hard, kubectl delete, and similar destructive operations. User can override each warning. Active for the current session only. Use when touching prod, debugging live systems, or working in a shared environment. Use when asked to "be careful", "safety mode", "prod mode", or "careful mode". NOT for scoping edits to a specific directory (see mk:freeze).

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Session-scoped directory edit restriction. Blocks Edit and Write outside the allowed path for the current session only. Use when debugging to prevent accidentally "fixing" unrelated code, or when you want to scope changes to one module. Use when asked to "freeze", "restrict edits", "only edit this folder", or "lock down edits". NOT for blocking destructive shell commands (see mk:careful).

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Build error triage: detect language, load fix patterns, auto-retry. Use for 'build failed', 'fix compilation', 'type error'. Chains into mk:verify. NOT for runtime errors (see mk:fix); NOT for architectural debugging (see mk:investigate).

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Use when answering factual or explanatory questions about the current project — codebase, architecture, conventions, workflows, constraints — with minimal cited evidence. Triggers on "how does X work here", "what does X mean", "why is X structured this way", "is this claim true in the repo", "explain X with sources". NOT for brainstorming or comparing approaches (mk:brainstorming), trade-off decisions (mk:party), debugging/root cause (mk:investigate), code review (mk:review), plans (mk:plan-creator), security audits (mk:cso), visual explanations/diagrams (mk:preview --explain), test-coverage gaps (mk:nyquist), library docs (mk:docs-finder), or workflow navigation (mk:help).

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Django Redis caching with django-cacheops. This skill should be used when implementing caching, adding cache invalidation, optimizing API performance, modifying models that affect cached data, or debugging cache-related issues in the Django backend.

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Structured logging conventions for DraftForge backend (Django/Celery/Daphne) and frontend (React). This skill should be used when adding log statements, creating new modules, debugging with logs, or reviewing logging patterns. Covers structlog usage, system/subsystem taxonomy, required fields, log levels, and Grafana query patterns.

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Routes development tasks to the correct language or framework expert agent. Use when user requests code review, implementation, refactoring, or debugging.

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Analyze reviewed Grafana log evidence for event patterns, error-rate changes, and enrolled security markers. Use when a user needs bounded log analytics for an incident window, error-log comparison, anomaly triage, operational debugging, or a cautious check of approved security signals.

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Use when encountering any bug, test failure, or unexpected behavior, before proposing fixes

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Bridge Codex to web-based AI model products by packaging local task context, scrub-checking it, sending it through an approved browser surface to ChatGPT Pro, Claude, Grok, Gemini, or another web model, waiting for the answer, and returning the model response to the user or Codex. Also guide DevSpace-like MCP Connector Mode when the user wants ChatGPT Pro or another MCP-capable web host to access approved local workspaces without relying on Codex browser automation. Use when the user asks for GPT Pro, ChatGPT Pro, Claude web, Grok, Gemini web, web model bridge, external model consult, ask another model, second opinion, use a web AI model, browserless agent access to GPT Pro, MCP connector, DevSpace-like workflow, or send local repo context to a browser-based model for planning, review, debugging, architecture discussion, or implementation guidance.

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Up-to-date Zig programming language patterns for version 0.17.0-dev (0.16.0 stable APIs plus the 0.17 deltas). Use when writing, reviewing, or debugging Zig code, working with build.zig and build.zig.zon files, or using comptime metaprogramming. Critical for avoiding outdated patterns from training data - especially std.net→std.Io.net (requires Io instance), std.time timestamps removed (use clock_gettime), std.Thread.Mutex/Condition/sleep removed (use pthreads), std.crypto.random removed, build system APIs (root_module, Compile methods→Module methods), I/O APIs (buffered writer pattern), container initialization (.empty/.init), allocator selection (DebugAllocator), ArrayList now unmanaged by default, @typeInfo lowercase fields (.@"struct" not .Struct), and removed language features (async/await, usingnamespace). Also covers 0.17.0-dev deltas: b.args→run_cmd.addPassthruArgs(), std.gpu→std.spirv, @bitCast logical-bit (endian-agnostic) semantics, build configurer/maker split, and the zig-pkg/ package directory. Also covers quality tooling Zig does not ship: coverage with kcov (and why in-file tests wreck the denominator), detecting unused private functions (neither the compiler nor zlint's unused-decls finds them), duplicate detection with jscpd, zlint (NOT the same-named X.509 linter in Homebrew), and the built-in fuzzer whose testOne now takes *std.testing.Smith rather than []const u8.

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Manages shadcn components and projects — adding, searching, fixing, debugging, styling, and composing UI, including chat interfaces. Provides project context, component docs, and usage examples. Applies when working with shadcn/ui, component registries, presets, --preset codes, or any project with a components.json file. Also triggers for "shadcn init", "create an app with --preset", or "switch to --preset".

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Normalizes and transforms RNA-seq count matrices for DE, visualization, clustering, and ML. Covers between-sample (TMM, TMMwsp, RLE/median-of-ratios, upper quartile), within-sample (TPM, FPKM/RPKM), variance-stabilizing (VST, rlog, log-CPM), GC-content correction (cqn, EDASeq), and single-cell (scran deconvolution, scanpy normalize_total). Encodes the composition-bias rationale, the "most genes not DE" assumption and its catastrophic failure modes (MYC amplification, apoptosis, viral host shutoff, prokaryotic stress), the "lengthScaledTPM is not TPM" naming trap, the "TPM is not for DE" rule, the blind=TRUE vs FALSE decision, ERCC spike-in normalization (SBN), and the single-cell zero-inflation breakdown of TMM/RLE. Use when choosing or applying normalization, debugging shifted-MA-plot diagnostics, handling zero-heavy single-cell data, or correcting GC bias.

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Imports gene expression count matrices from featureCounts, HTSeq, STAR ReadsPerGene, Salmon/kallisto via tximport or tximeta, RSEM, 10X Genomics MTX/H5, AnnData H5AD, and RDS. Handles silent-miscounting traps (featureCounts -p v2.0.2 API break, STAR strandedness column choice, salmon NumReads-sum without tximport, RSEM non-integer expected_count, GENCODE _PAR_Y suffix, zero-length-transcript TPM divide-by-zero), and encodes the tximport countsFromAbundance decision tree with the "lengthScaledTPM is not TPM" warning. Use when assembling a gene-by-sample count matrix from aligner or quantifier output, importing salmon/kallisto for DESeq2 vs limma-voom, choosing strandedness column for STAR, debugging zero-count panics, or building tx2gene mapping.

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Stores and operates on sparse expression matrices for single-cell and large bulk RNA-seq, covering dgCMatrix/dgRMatrix/dgTMatrix when-each-is-fast, the dgCMatrix (CSC, R) <-> CSR (Python) implicit transpose, AnnData (cells-rows) <-> SingleCellExperiment (cells-cols) orientation flip, HDF5/h5ad vs Zarr cloud-native shift, HDF5SummarizedExperiment + DelayedArray for out-of-memory bulk, scanpy backed mode for large h5ad, the ~10-15% density crossover where dense beats sparse, 10X format proliferation (MTX vs CellRanger H5 vs h5ad), the dense-conversion memory blow-up, and Dask + Zarr for consortium-scale matrices. Use when choosing sparse format, working with single-cell-sized matrices, importing/exporting 10X, debugging R/Python interop transposes, processing matrices too large for RAM, or building cloud-native pipelines.

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Analyzes pooled CRISPR screens with MAGeCK (Li et al 2014), covering count generation (mageck count), the RRA two-condition workflow (mageck test using alpha-RRA over per-sgRNA negative-binomial p-values), the MLE multi-condition workflow (mageck mle with explicit design matrix and beta-score output), normalization choice (median vs total vs control-sgRNA vs spike-in), sgRNA efficiency injection, paired-sample testing, time-course design, drug-screen versus dropout-screen design matrices, MAGeCKFlute and MAGeCK-VISPR downstream visualization, and decision logic for when to use MAGeCK vs JACKS / BAGEL2 / drugZ / Chronos. Use when running a fresh CRISPR screen analysis, picking RRA vs MLE for the experimental design, choosing a normalization method from QC signatures, debugging MLE convergence failure or NaN beta scores, comparing MAGeCK output across tools, or building a batch-aware multi-cell-line / multi-condition MLE design matrix.

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Quantifies CRISPR editing outcomes with CRISPResso2 (Clement 2019 Nat Biotechnol) across Cas9-nuclease (indels, HDR), CBE and ABE base editors (target conversion + bystander), and prime editor (pegRNA-templated) modes. Covers single-amplicon (CRISPResso), multi-sample batch (CRISPRessoBatch), pooled-amplicon (CRISPRessoPooled), WGS off-target (CRISPRessoWGS), and sample-comparison (CRISPRessoCompare) workflows; quantification-window math that controls what is called edited; substitution-vs-indel diagnostic to distinguish BE from Cas9 contamination; MMEJ deletion pattern interpretation; allele-frequency tables; and failure modes from amplicon misalignment or contamination. Use when quantifying editing from amplicon sequencing, choosing CRISPResso mode by design, distinguishing intended edits from bystanders and indel byproducts, debugging low-alignment runs, or generating publication-grade editing reports.

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Master authentication and authorization patterns including JWT, OAuth2, session management, and RBAC to build secure, scalable access control systems. Use when implementing auth systems, securing APIs, or debugging security issues.

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Testing patterns for PHPUnit and Playwright E2E tests. Use when writing tests, debugging test failures, setting up test coverage, or implementing test patterns for ActivityPub features.

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Core Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tables, time systems, WCS, and cosmology. Use when implementing or debugging astronomical data analysis code with Astropy.

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