/* GSR Data Delivery Portal — shared design tokens
   Original design inspired by institutional academic web aesthetics.
   Palette: Pine green primary, warm parchment neutrals, deep ink text. */

:root {
  /* Pine green family (primary) */
  --pine-900: #003c23;
  --pine-800: #00532f;
  --pine-700: #00693e;   /* primary */
  --pine-600: #1a7c52;
  --pine-500: #3a9168;
  --pine-100: #e3eee7;
  --pine-50:  #f1f6f2;

  /* Warm neutrals */
  --ink-900: #0f1a14;
  --ink-700: #2a352e;
  --ink-500: #5a6360;
  --ink-400: #8a9290;
  --ink-300: #b8bfba;

  --paper-100: #ffffff;
  --paper-200: #faf9f4;   /* parchment */
  --paper-300: #f3f1e8;
  --paper-400: #ebe8db;

  --border-100: #ece9dd;
  --border-200: #ddd8c5;
  --border-300: #c8c2ab;

  /* Status */
  --warn-500: #b07b00;
  --warn-100: #fbf3dc;
  --danger-500: #a8331f;
  --danger-100: #fae6df;
  --info-500: #265d99;

  /* Type */
  --font-display: "Source Serif 4", "Source Serif Pro", Georgia, serif;
  --font-ui: "Inter", system-ui, -apple-system, sans-serif;
  --font-mono: "JetBrains Mono", ui-monospace, "SF Mono", Menlo, monospace;
}

* { box-sizing: border-box; }

.portal {
  font-family: var(--font-ui);
  color: var(--ink-900);
  background: var(--paper-200);
  font-size: 14px;
  line-height: 1.5;
  -webkit-font-smoothing: antialiased;
}

.portal a { color: var(--pine-700); text-decoration: none; }
.portal a:hover { text-decoration: underline; }

.serif { font-family: var(--font-display); font-weight: 400; letter-spacing: -0.005em; }
.mono { font-family: var(--font-mono); }

/* Buttons */
.btn {
  display: inline-flex; align-items: center; gap: 8px;
  height: 34px; padding: 0 14px;
  border-radius: 4px;
  font: 500 13px/1 var(--font-ui);
  border: 1px solid var(--border-200);
  background: var(--paper-100);
  color: var(--ink-900);
  cursor: pointer;
  transition: background .12s, border-color .12s, color .12s;
}
.btn:hover { background: var(--paper-300); border-color: var(--border-300); }
.btn-primary { background: var(--pine-700); color: #fff; border-color: var(--pine-700); }
.btn-primary:hover { background: var(--pine-800); border-color: var(--pine-800); }
.btn-ghost { background: transparent; border-color: transparent; }
.btn-ghost:hover { background: var(--paper-300); }
.btn-sm { height: 28px; padding: 0 10px; font-size: 12px; }

/* Inputs */
.input {
  height: 34px; padding: 0 12px;
  border: 1px solid var(--border-200);
  background: var(--paper-100);
  border-radius: 4px;
  font: 400 13px/1 var(--font-ui);
  color: var(--ink-900);
  outline: none;
}
.input:focus { border-color: var(--pine-700); box-shadow: 0 0 0 3px var(--pine-100); }

/* Pills / tags */
.tag {
  display: inline-flex; align-items: center; gap: 6px;
  height: 22px; padding: 0 8px;
  border-radius: 3px;
  font: 500 11px/1 var(--font-ui);
  letter-spacing: 0.02em;
  text-transform: uppercase;
  background: var(--paper-300);
  color: var(--ink-700);
  border: 1px solid var(--border-200);
}
.tag-pine { background: var(--pine-100); color: var(--pine-800); border-color: transparent; }
.tag-warn { background: var(--warn-100); color: var(--warn-500); border-color: transparent; }
.tag-danger { background: var(--danger-100); color: var(--danger-500); border-color: transparent; }
.tag-muted { background: transparent; color: var(--ink-500); border-color: var(--border-200); }

/* Hairlines and decorative */
.hr { height: 1px; background: var(--border-100); border: 0; }
.divider-rule {
  height: 4px;
  background:
    linear-gradient(var(--pine-700), var(--pine-700)) top/100% 1px no-repeat,
    linear-gradient(var(--pine-700), var(--pine-700)) bottom/100% 2px no-repeat;
  background-color: transparent;
}

/* Filename icon swatches (no real icons — flat 2-letter glyphs) */
.fglyph {
  width: 28px; height: 28px;
  border-radius: 3px;
  display: inline-flex; align-items: center; justify-content: center;
  font: 600 10px/1 var(--font-mono);
  letter-spacing: 0.04em;
  flex: 0 0 28px;
}
.fglyph-dir   { background: var(--pine-100); color: var(--pine-800); }
.fglyph-md    { background: var(--paper-400); color: var(--ink-700); }
.fglyph-txt   { background: var(--paper-400); color: var(--ink-700); }
.fglyph-csv   { background: var(--paper-400); color: var(--ink-700); }
.fglyph-tiff  { background: #efe6da; color: #6b4f1a; }
.fglyph-archived { background: #ece9dd; color: var(--ink-400); }
/* Genomics-specific file types */
.fglyph-fastq   { background: #dde9d4; color: #2f5d2a; }   /* sage green — raw reads */
.fglyph-bam     { background: #d6e3da; color: #1f4d34; }   /* darker pine — alignments */
.fglyph-vcf     { background: #e8e0e8; color: #4a2a4a; }   /* mauve — variants */
.fglyph-idat    { background: #f0e6d2; color: #5a4218; }   /* tan — methylation arrays */
.fglyph-ont     { background: #e8d6e3; color: #5a2a48; }   /* plum — Nanopore */
.fglyph-archive { background: #e6e0d6; color: #5a4a2a; }   /* paper-tan — tar/zip */
.fglyph-pdf     { background: #f0d8d4; color: #6a2a1a; }   /* terracotta — PDFs */
.fglyph-config  { background: var(--paper-400); color: var(--ink-500); }
.fglyph-html    { background: var(--paper-400); color: var(--ink-500); }
.fglyph-file    { background: var(--paper-300); color: var(--ink-500); }

/* Clickable rows in the per-project Contents tree.
   Wraps an <a> around the same flex layout used by .crow,
   adds hover affordance, removes default link styling. */
a.crow-link { text-decoration: none; color: inherit; cursor: pointer;
              padding-left: 4px; padding-right: 4px;
              margin-left: -4px; margin-right: -4px; border-radius: 3px; }
a.crow-link:hover { background: var(--paper-200); }
a.crow-link:hover .nm { color: var(--pine-700); text-decoration: underline; }

/* Striped placeholder for the seal/imagery */
.placeholder-stripes {
  background-image: repeating-linear-gradient(
    -45deg,
    var(--paper-300) 0 8px,
    var(--paper-400) 8px 16px
  );
  border: 1px solid var(--border-200);
}

/* Scroll niceties */
.scroll-y { overflow-y: auto; }
.scroll-y::-webkit-scrollbar { width: 10px; }
.scroll-y::-webkit-scrollbar-thumb { background: var(--border-200); border-radius: 8px; }
.scroll-y::-webkit-scrollbar-track { background: transparent; }