Fix ProForma writer for ranges bearing multiple modifications (§4.5)

[trishorts]

Problem

ProFormaWriter.WriteString throws ProFormaParseException: "Can't nest ranges within each other." whenever a term contains a sequence range that carries more than one modification — the ProForma 2.0 §4.5 construct (SEQ)[mod1][mod2]…. The parser accepts these strings, so they cannot currently be round-tripped: parsing succeeds but writing the resulting term fails.

Reproduce

var parser = new ProFormaParser();
var writer = new ProFormaWriter();
var term = parser.ParseString("PRT(ESFRMS)[Oxidation][Oxidation][half cystine][half cystine]ISK");
writer.WriteString(term);   // throws: Can't nest ranges within each other.

This also blocks real specification examples (e.g. the §4.5 insulin-style range bearing multiple oxidations and half-cystines).

Root cause

Each modification on a range is parsed as a separate ProFormaTag spanning the same (ZeroBasedStartIndex, ZeroBasedEndIndex) — the parser keeps the range open across consecutive )[mod][mod] until the next residue resets it. When the writer reaches the range, its inner loop scans the tags that fall within the range and unconditionally throws for any whose start != end. But a co-located range modification legitimately has start != end (it spans the whole range), so these were mistaken for nested ranges.

Fix

In the range branch of WriteString, a tag whose start and end equal the current range's start and end is treated as another modification on that same range and emitted as a consecutive [descriptor] after the range closes. Genuinely nested ranges (a different start != end inside the range) still throw as before.

After

PRT(ESFRMS)[Oxidation][Oxidation][half cystine][half cystine]ISK   // round-trips unchanged
SE(QUEN)[+14.05][Oxidation]CE                                       // two modifications on one range

Tests

• WriteMultipleModificationsOnSameRange — constructs a range carrying two modifications and asserts SE(QUEN)[+14.05][Oxidation]CE.
• RoundTripMultipleModificationsOnRange — parse→write round-trip of a four-modification range.
• Full suite green: 235 passed, 7 skipped, 0 failed (net472 + net6.0).

🤖 Generated with Claude Code

https://claude.ai/code/session_01JNnpzBNwfnTbZxtZdtAzLG

[rfellers]

looks great, thanks!

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 89.43%. Comparing base (b4d1949) to head (291403e).
⚠️ Report is 3 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #116      +/-   ##
==========================================
+ Coverage   89.23%   89.43%   +0.20%     
==========================================
  Files         103      105       +2     
  Lines        5721     5851     +130     
  Branches      882      912      +30     
==========================================
+ Hits         5105     5233     +128     
- Misses        429      430       +1     
- Partials      187      188       +1     

Files with missing lines	Coverage Δ
src/TopDownProteomics/ProForma/ProFormaWriter.cs	93.29% <100.00%> (+4.24%)	⬆️

... and 4 files with indirect coverage changes

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