@tiagojct/subsub 0.5.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +90 -0
- package/bin/subsub-bench.js +19 -0
- package/bin/subsub.js +14 -0
- package/dist/args.js +67 -0
- package/dist/bench.js +534 -0
- package/dist/bridge.js +107 -0
- package/dist/cli.js +209 -0
- package/dist/config.js +144 -0
- package/dist/doctor.js +131 -0
- package/dist/init.js +215 -0
- package/dist/look.js +107 -0
- package/dist/paths.js +86 -0
- package/dist/preview.js +94 -0
- package/dist/profiles.js +79 -0
- package/dist/prompt.js +72 -0
- package/dist/roles.js +73 -0
- package/dist/subsub.js +414 -0
- package/docs/Subsub.md +126 -0
- package/extensions/subsub.ts +6 -0
- package/package.json +73 -0
- package/prompts/alert.md +4 -0
- package/prompts/clean-tags.md +4 -0
- package/prompts/gaps.md +5 -0
- package/prompts/import-queue.md +5 -0
- package/prompts/lit-note.md +5 -0
- package/prompts/manuscript.md +5 -0
- package/prompts/synthesis.md +5 -0
- package/prompts/tag-batch.md +5 -0
- package/roles/librarian.md +46 -0
- package/roles/researcher.md +37 -0
- package/scripts/build.mjs +14 -0
- package/scripts/make-themes.py +116 -0
- package/src/args.ts +64 -0
- package/src/bench.ts +580 -0
- package/src/bridge.ts +134 -0
- package/src/cli.ts +201 -0
- package/src/config.ts +191 -0
- package/src/doctor.ts +171 -0
- package/src/init.ts +252 -0
- package/src/look.ts +141 -0
- package/src/paths.ts +100 -0
- package/src/preview.ts +107 -0
- package/src/profiles.ts +99 -0
- package/src/prompt.ts +81 -0
- package/src/roles.ts +83 -0
- package/src/subsub.ts +434 -0
- package/templates/Zotero agent.md +87 -0
- package/templates/vocabularies/any-field.md +52 -0
- package/templates/vocabularies/health-informatics.md +88 -0
- package/templates/vocabularies/health-sciences.md +95 -0
- package/themes/subsub-glauca-dark.json +91 -0
- package/themes/subsub-glauca-light.json +91 -0
- package/themes/subsub-try-works-dark.json +91 -0
- package/themes/subsub-try-works-light.json +91 -0
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---
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required_facets: topic, status
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single_facets: status
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max_per_facet: topic=4, type=2
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---
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Tag list for the Zotero library (health sciences). Sub-Sub reads this file and refuses any tag that is not listed here. Add, rename or remove tags as your library needs: one tag per bullet, in backticks, then a short description. Put old or alternative names after "aliases:"; the librarian uses them to map old tags.
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## topic
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What the item is about. 1 to 4 per item.
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- `topic/cardiovascular` Heart and blood vessels. aliases: cardiology, hypertension
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- `topic/respiratory` Lungs and airways. aliases: pulmonology, asthma, COPD
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- `topic/neurology` Brain and nervous system. aliases: stroke, dementia
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- `topic/mental-health` Psychiatry and mental health. aliases: psychiatry, depression, anxiety
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- `topic/oncology` Cancer. aliases: cancer
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- `topic/infectious-disease` Infections and vaccines. aliases: infection, vaccination, COVID-19
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- `topic/endocrinology` Diabetes, obesity and hormones. aliases: diabetes, obesity
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- `topic/gastroenterology` Digestive system and liver. aliases: hepatology
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- `topic/nephrology` Kidneys and urinary tract. aliases: kidney
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- `topic/musculoskeletal` Bones, joints and muscles. aliases: rheumatology, orthopaedics
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- `topic/immunology` Immune system and allergy. aliases: allergy
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- `topic/haematology` Blood. aliases: hematology
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- `topic/reproductive-health` Obstetrics, gynaecology and sexual health. aliases: obstetrics, gynecology, pregnancy
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- `topic/pediatrics` Children and adolescents. aliases: paediatrics, children
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- `topic/ageing` Older adults and ageing. aliases: aging, geriatrics
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- `topic/critical-care` Intensive care and emergency medicine. aliases: ICU, emergency
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- `topic/surgery` Surgery and anaesthesia. aliases: anesthesia
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- `topic/pharmacology` Drugs and their effects. aliases: pharmacotherapy, drugs
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- `topic/genetics` Genetics and genomics. aliases: genomics
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- `topic/nutrition` Nutrition and diet. aliases: diet
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- `topic/physiology` Normal function of the body. aliases: human physiology
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- `topic/public-health` Public health and prevention. aliases: prevention
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- `topic/epidemiology` Epidemiology and population studies.
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- `topic/health-services` Organisation, quality and costs of health care. aliases: health care quality, health economics
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- `topic/health-policy` Health policy and regulation. aliases: regulation
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- `topic/medical-education` Education of health professionals. aliases: medical education
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- `topic/ethics` Ethics in medicine and research. aliases: bioethics
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- `topic/digital-health` Digital health, eHealth and mHealth. aliases: eHealth, mHealth, telemedicine
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- `topic/artificial-intelligence` AI in health. aliases: AI, LLM, machine learning
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- `topic/statistics` Statistics and data analysis as a subject: methods, teaching, textbooks. aliases: biostatistics
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- `topic/research-methods` Research methods, reporting, integrity and meta-research. aliases: methodology, reproducibility
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- `topic/history-of-medicine` History of medicine. aliases: history
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## method
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How the work was done. Only when it applies.
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- `method/statistical-modelling` The work fits regression or other statistical models. A paper or book about statistics gets topic/statistics instead. aliases: regression
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- `method/machine-learning` The work trains or evaluates machine-learning models (not a paper about AI in general). aliases: ML, machine learning
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- `method/nlp` Natural language processing. aliases: NLP, text mining
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- `method/survey` Questionnaire survey. aliases: questionnaire
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- `method/interviews` Interviews and focus groups. aliases: focus groups
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- `method/delphi` Delphi or consensus method. aliases: consensus
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- `method/psychometrics` Instrument development and validation.
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- `method/usability-testing` Usability and user testing. aliases: usability
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- `method/simulation` Simulation or modelling study.
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- `method/laboratory` Laboratory or bench experiments, including animal studies. aliases: in vitro, in vivo
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- `method/imaging` Medical imaging is the main source of data. aliases: MRI, CT, ultrasound
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- `method/programming` Programming and software tools. aliases: programming, R, Python
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## type
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What kind of study or document it is.
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- `type/rct` The item reports a randomised controlled trial (not a review or commentary about trials). aliases: RCT, Randomized Controlled Trial
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- `type/cohort` Cohort study. aliases: Cohort Studies, longitudinal
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- `type/case-control` Case-control study.
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- `type/cross-sectional` Cross-sectional study. aliases: Cross-Sectional Studies
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- `type/diagnostic-accuracy` Diagnostic accuracy study.
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- `type/validation-study` Validation study (instrument, model or equation).
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- `type/qualitative` Qualitative study.
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- `type/mixed-methods` Mixed-methods study.
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- `type/systematic-review` Systematic review. aliases: Systematic Review
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- `type/meta-analysis` Meta-analysis. aliases: Meta-Analysis
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- `type/scoping-review` Scoping review.
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- `type/narrative-review` Narrative review. aliases: Review
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- `type/guideline` The item is a guideline, statement or technical standard (not a paper about guidelines). aliases: Practice Guideline
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- `type/protocol` Study protocol.
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- `type/editorial` Editorial, commentary, letter or book review. aliases: Editorial, Comment, Letter
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- `type/case-report` Case report.
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- `type/web-document` Web page, blog post or online document. aliases: blog post
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- `type/technical-report` Technical or institutional report.
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- `type/thesis` Thesis or dissertation.
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- `type/textbook` Textbook.
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- `type/monograph` Monograph or non-fiction book.
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- `type/edited-book` Edited book or book chapter.
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## status
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Reading status. Exactly one per item.
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- `status/to-read` Not read yet.
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- `status/reading` Reading now.
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- `status/read` Read.
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{
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"$schema": "https://raw.githubusercontent.com/earendil-works/pi/main/packages/coding-agent/src/modes/interactive/theme/theme-schema.json",
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"name": "subsub-glauca-dark",
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"vars": {
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"bg": "#10161c",
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"surface": "#171f26",
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"raised": "#1f2932",
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"text": "#e8eef2",
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"muted": "#8c8c8c",
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"line": "#2a3540",
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"mark": "#3d97ff",
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"markBright": "#6cb2ff",
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"markDeep": "#007aff",
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"toneDeep": "#142430",
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"tone": "#2b4356",
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"toneBright": "#4d7391",
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"tonePale": "#93b7c9",
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"green": "#62ba46",
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"red": "#b85f5f",
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"yellow": "#c79a3d",
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"violet": "#b184db",
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"link": "#4a9edb",
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"dim": "#616365",
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"select": "#2b4356",
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"okBg": "#22352a",
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"errBg": "#31292f"
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},
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"colors": {
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"accent": "mark",
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"border": "toneBright",
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"borderAccent": "mark",
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"borderMuted": "line",
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"success": "green",
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"error": "red",
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"warning": "yellow",
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"muted": "muted",
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"dim": "dim",
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"text": "text",
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"thinkingText": "muted",
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"selectedBg": "select",
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"scrollbarTrack": "line",
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"scrollbarThumb": "muted",
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"searchMatchBg": "select",
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"searchMatchText": "text",
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"userMessageBg": "raised",
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"userMessageText": "text",
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"customMessageBg": "surface",
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"customMessageText": "text",
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"customMessageLabel": "tonePale",
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"toolPendingBg": "surface",
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"toolSuccessBg": "okBg",
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"toolErrorBg": "errBg",
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"toolTitle": "text",
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"toolOutput": "muted",
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"mdHeading": "tonePale",
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"mdLink": "link",
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"mdLinkUrl": "dim",
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"mdCode": "green",
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"mdCodeBlock": "text",
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"mdCodeBlockBorder": "line",
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"mdQuote": "muted",
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"mdQuoteBorder": "toneBright",
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"mdHr": "line",
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"mdListBullet": "toneBright",
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"toolDiffAdded": "green",
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"toolDiffRemoved": "red",
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"toolDiffContext": "muted",
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"syntaxComment": "#8c8c8c",
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"syntaxKeyword": "#007aff",
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"syntaxFunction": "#4a9edb",
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"syntaxVariable": "#e8eef2",
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"syntaxString": "#62ba46",
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"syntaxNumber": "#b184db",
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"syntaxType": "#45a3ad",
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"syntaxOperator": "#a7b1b8",
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"syntaxPunctuation": "#86929a",
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"thinkingOff": "line",
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"thinkingMinimal": "dim",
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"thinkingLow": "toneBright",
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"thinkingMedium": "tonePale",
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"thinkingHigh": "violet",
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"thinkingXhigh": "markBright",
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"thinkingMax": "mark",
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"bashMode": "mark"
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},
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"export": {
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"pageBg": "#10161c",
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"cardBg": "#171f26",
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"infoBg": "#1f2932"
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}
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}
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{
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"$schema": "https://raw.githubusercontent.com/earendil-works/pi/main/packages/coding-agent/src/modes/interactive/theme/theme-schema.json",
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"name": "subsub-glauca-light",
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"vars": {
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"bg": "#f0f4f6",
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"surface": "#f7fafb",
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"raised": "#ffffff",
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"text": "#16222a",
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"muted": "#55646d",
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"line": "#cdd7dc",
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"mark": "#0b62cf",
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"markBright": "#007aff",
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"markDeep": "#084b96",
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"toneDeep": "#16303f",
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"tone": "#35576b",
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"toneBright": "#3e6d84",
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"tonePale": "#b7cdd6",
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"green": "#3c6e38",
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"red": "#a55859",
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"yellow": "#846c36",
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"violet": "#6b588b",
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"link": "#33668b",
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"dim": "#8b969d",
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"select": "#b7cdd6",
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"okBg": "#dde6e0",
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"errBg": "#eae0e1"
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},
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"colors": {
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"accent": "mark",
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"border": "toneBright",
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"borderAccent": "mark",
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"borderMuted": "line",
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"success": "green",
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"error": "red",
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"warning": "yellow",
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"muted": "muted",
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"dim": "dim",
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"text": "text",
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"thinkingText": "muted",
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"selectedBg": "select",
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"scrollbarTrack": "line",
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"scrollbarThumb": "muted",
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"searchMatchBg": "select",
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"searchMatchText": "text",
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"userMessageBg": "raised",
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"userMessageText": "text",
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"customMessageBg": "surface",
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"customMessageText": "text",
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"customMessageLabel": "tone",
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"toolPendingBg": "surface",
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"toolSuccessBg": "okBg",
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"toolErrorBg": "errBg",
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"toolTitle": "text",
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"toolOutput": "muted",
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"mdHeading": "tone",
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"mdLink": "link",
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"mdLinkUrl": "dim",
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"mdCode": "green",
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"mdCodeBlock": "text",
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"mdCodeBlockBorder": "line",
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"mdQuote": "muted",
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"mdQuoteBorder": "toneBright",
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"mdHr": "line",
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"mdListBullet": "toneBright",
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"toolDiffAdded": "green",
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"toolDiffRemoved": "red",
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"toolDiffContext": "muted",
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"syntaxComment": "#55646d",
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"syntaxKeyword": "#0b62cf",
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"syntaxFunction": "#33668b",
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"syntaxVariable": "#16222a",
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"pageBg": "#f0f4f6",
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{
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"$schema": "https://raw.githubusercontent.com/earendil-works/pi/main/packages/coding-agent/src/modes/interactive/theme/theme-schema.json",
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"name": "subsub-try-works-dark",
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"vars": {
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"bg": "#12161b",
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"surface": "#1b2127",
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"raised": "#232b32",
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"text": "#f1efe9",
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"muted": "#97a0a4",
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"line": "#2c3640",
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"mark": "#c9651d",
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"markBright": "#e0832a",
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"markDeep": "#9a4a16",
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"toneDeep": "#14242c",
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"tone": "#2c4953",
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"toneBright": "#4d7680",
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"tonePale": "#8fb6bd",
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"green": "#86a87f",
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"red": "#c05a3a",
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"yellow": "#c9651d",
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"violet": "#a487ba",
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"link": "#5f93b0",
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"dim": "#687074",
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"select": "#2c4953",
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"okBg": "#2a3433",
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"errBg": "#352a2a"
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},
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"colors": {
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"accent": "mark",
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"border": "toneBright",
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"borderAccent": "mark",
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"borderMuted": "line",
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"success": "green",
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"error": "red",
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"warning": "yellow",
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"muted": "muted",
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"dim": "dim",
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"text": "text",
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"thinkingText": "muted",
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"selectedBg": "select",
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"scrollbarTrack": "line",
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"scrollbarThumb": "muted",
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"searchMatchBg": "select",
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"searchMatchText": "text",
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"userMessageBg": "raised",
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"userMessageText": "text",
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"customMessageBg": "surface",
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"customMessageText": "text",
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"customMessageLabel": "tonePale",
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"toolPendingBg": "surface",
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"toolSuccessBg": "okBg",
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"toolErrorBg": "errBg",
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"toolTitle": "text",
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"toolOutput": "muted",
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"mdHeading": "tonePale",
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"mdLink": "link",
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"mdLinkUrl": "dim",
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"mdCode": "green",
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"mdCodeBlock": "text",
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"mdCodeBlockBorder": "line",
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"mdQuote": "muted",
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"mdQuoteBorder": "toneBright",
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"mdHr": "line",
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"mdListBullet": "toneBright",
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"toolDiffAdded": "green",
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"toolDiffRemoved": "red",
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"toolDiffContext": "muted",
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"syntaxComment": "#97a0a4",
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"syntaxKeyword": "#c9651d",
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"syntaxFunction": "#5f93b0",
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"syntaxVariable": "#f1efe9",
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"syntaxString": "#86a87f",
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"syntaxNumber": "#a487ba",
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"syntaxType": "#5f97a0",
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"syntaxOperator": "#aeb6b8",
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"syntaxPunctuation": "#8a9296",
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"thinkingOff": "line",
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"thinkingMinimal": "dim",
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"thinkingLow": "toneBright",
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"thinkingMedium": "tonePale",
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"thinkingHigh": "violet",
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"thinkingXhigh": "markBright",
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"thinkingMax": "mark",
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"bashMode": "mark"
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},
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"export": {
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"pageBg": "#12161b",
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"cardBg": "#1b2127",
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"infoBg": "#232b32"
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"name": "subsub-try-works-light",
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"vars": {
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"bg": "#dee7e4",
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"surface": "#e7efeb",
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"raised": "#f2f7f4",
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"text": "#18272b",
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"muted": "#52646a",
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"line": "#c4d2cd",
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"mark": "#9e5017",
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"markBright": "#b85f1c",
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"markDeep": "#7a3a10",
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"toneDeep": "#16242b",
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"tone": "#264852",
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"toneBright": "#3d6b76",
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"tonePale": "#b4ccc9",
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"green": "#4f6855",
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"red": "#c05a3a",
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"yellow": "#c9651d",
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"violet": "#655c7a",
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"link": "#3f6274",
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"dim": "#839295",
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"select": "#b4ccc9",
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"okBg": "#d2dcd6",
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"errBg": "#e1d7cf"
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},
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"colors": {
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"accent": "mark",
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"border": "toneBright",
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"borderAccent": "mark",
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"borderMuted": "line",
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"success": "green",
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"error": "red",
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"warning": "yellow",
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"muted": "muted",
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"dim": "dim",
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"text": "text",
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"thinkingText": "muted",
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"selectedBg": "select",
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"scrollbarTrack": "line",
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"scrollbarThumb": "muted",
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"searchMatchBg": "select",
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"searchMatchText": "text",
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"userMessageBg": "raised",
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"userMessageText": "text",
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"customMessageBg": "surface",
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"customMessageText": "text",
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"customMessageLabel": "tone",
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"toolPendingBg": "surface",
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"toolSuccessBg": "okBg",
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"toolErrorBg": "errBg",
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"toolTitle": "text",
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"toolOutput": "muted",
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"mdHeading": "tone",
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"mdLink": "link",
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"mdLinkUrl": "dim",
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"mdCode": "green",
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"mdCodeBlock": "text",
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"mdCodeBlockBorder": "line",
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"mdQuote": "muted",
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"mdQuoteBorder": "toneBright",
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"mdHr": "line",
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"mdListBullet": "toneBright",
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"toolDiffAdded": "green",
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"toolDiffRemoved": "red",
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"toolDiffContext": "muted",
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"syntaxComment": "#52646a",
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"syntaxKeyword": "#9e5017",
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"syntaxFunction": "#3f6274",
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"syntaxVariable": "#18272b",
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"syntaxString": "#4f6855",
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"syntaxNumber": "#655c7a",
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"syntaxType": "#3f656b",
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"syntaxOperator": "#52646a",
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"syntaxPunctuation": "#52646a",
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"thinkingOff": "line",
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"thinkingMinimal": "dim",
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"thinkingLow": "toneBright",
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"thinkingMedium": "tone",
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"thinkingHigh": "violet",
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"thinkingXhigh": "markBright",
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"thinkingMax": "mark",
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"bashMode": "mark"
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},
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"export": {
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"pageBg": "#dee7e4",
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"cardBg": "#e7efeb",
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"infoBg": "#f2f7f4"
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}
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}
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