apps, docs, tools: link app readmes instead of their directories

apps/01-hello-c/README.md

@@ -1,8 +1,8 @@
 # 01 - hello, C
 
-[01-hello-rust](../01-hello-rust) written in C. C apps build with a WASI clang
-toolchain rather than Emscripten, because Emscripten's standalone modules can't
-open the files an Ark mounts.
+[01-hello-rust](../01-hello-rust/README.md) written in C. C apps build with a
+WASI clang toolchain rather than Emscripten, because Emscripten's standalone
+modules can't open the files an Ark mounts.
 
 The Makefile finds a wasi-sdk install at `/opt/wasi-sdk`, or falls back to
 Homebrew's WASI toolchain. `WASI_SDK` points it at any other clang that carries

apps/01-hello-go/README.md

@@ -1,7 +1,7 @@
 # 01 - hello, Go
 
-[01-hello-rust](../01-hello-rust) written in Go. The Makefile builds Go apps
-with TinyGo, which produces a module a fraction of the size the standard
+[01-hello-rust](../01-hello-rust/README.md) written in Go. The Makefile builds
+Go apps with TinyGo, which produces a module a fraction of the size the standard
 toolchain emits.
 
 ## Build and run

apps/01-hello-python/README.md

@@ -1,8 +1,8 @@
 # 01 - hello, Python
 
-[01-hello-rust](../01-hello-rust) written in Python. The module carries a
-trimmed CPython along with the app, so it is megabytes where the others are
-kilobytes, and it takes noticeably longer to start on an Ark.
+[01-hello-rust](../01-hello-rust/README.md) written in Python. The module
+carries a trimmed CPython along with the app, so it is megabytes where the
+others are kilobytes, and it takes noticeably longer to start on an Ark.
 
 The first Python build compiles that interpreter once and reuses it for every
 Python app. [05-running.md](../../docs/05-running.md) covers what it needs.

apps/01-hello-rust/README.md

@@ -2,8 +2,8 @@
 
 The smallest Ark app. It prints its manifest when run with no arguments and a
 greeting when given a data directory, and it reads no data. Start here, then
-compare the [Go](../01-hello-go), [C](../01-hello-c) and
-[Python](../01-hello-python) versions.
+compare the [Go](../01-hello-go/README.md), [C](../01-hello-c/README.md) and
+[Python](../01-hello-python/README.md) versions.
 
 ## Build and run
 

apps/04-cilantro-mini-c/README.md

@@ -1,9 +1,9 @@
 # 04 - cilantro-mini (C)
 
-[04-cilantro-mini-rust](../04-cilantro-mini-rust) written in C. Only
+[04-cilantro-mini-rust](../04-cilantro-mini-rust/README.md) written in C. Only
 `errno == ENOENT` means no answer, and any other failure to open or read a file
 stops the app. Each file is read into a buffer that grows to fit, since a
-genotype can hold long alleles. [01-hello-c](../01-hello-c) covers the
+genotype can hold long alleles. [01-hello-c](../01-hello-c/README.md) covers the
 toolchain.
 
 ## Build and run

apps/04-cilantro-mini-go/README.md

@@ -1,7 +1,8 @@
 # 04 - cilantro-mini (Go)
 
-[04-cilantro-mini-rust](../04-cilantro-mini-rust) written in Go. It distinguishes
-an absent genotype from a failed read with `errors.Is(err, fs.ErrNotExist)`.
+[04-cilantro-mini-rust](../04-cilantro-mini-rust/README.md) written in Go. It
+distinguishes an absent genotype from a failed read with
+`errors.Is(err, fs.ErrNotExist)`.
 
 ## Build and run
 

apps/04-cilantro-mini-python/README.md

@@ -1,9 +1,10 @@
 # 04 - cilantro-mini (Python)
 
-[04-cilantro-mini-rust](../04-cilantro-mini-rust) written in Python. An absent
-genotype arrives as `FileNotFoundError` and reads as no answer, while every
-other `OSError` stops the app. [01-hello-python](../01-hello-python) covers what
-a Python module costs.
+[04-cilantro-mini-rust](../04-cilantro-mini-rust/README.md) written in Python.
+An absent genotype arrives as `FileNotFoundError` and reads as no answer, while
+every other `OSError` stops the app.
+[01-hello-python](../01-hello-python/README.md) covers what a Python module
+costs.
 
 ## Build and run
 

apps/04-cilantro-mini-rust/README.md

@@ -10,9 +10,11 @@ makes the count inconclusive. An absent genotype is reported as no answer, never
 as two reference alleles. Any other read error stops the app.
 [04-reading-data.md](../../docs/04-reading-data.md) explains why.
 
-The same mini exists in [Go](../04-cilantro-mini-go),
-[C](../04-cilantro-mini-c) and [Python](../04-cilantro-mini-python), and
-[04-cilantro-soapiness](../04-cilantro-soapiness) turns it into a report.
+The same mini exists in [Go](../04-cilantro-mini-go/README.md),
+[C](../04-cilantro-mini-c/README.md) and
+[Python](../04-cilantro-mini-python/README.md), and
+[04-cilantro-soapiness](../04-cilantro-soapiness/README.md) turns it into a
+report.
 
 ## Build and run
 

apps/04-cilantro-soapiness/README.md

@@ -1,12 +1,13 @@
 # 04 - cilantro-soapiness
 
-The single variant from [04-cilantro-mini-rust](../04-cilantro-mini-rust),
-turned into a full report in the shape [06-reports.md](../../docs/06-reports.md)
-describes, with a finding, the evidence behind it, the method, its limitations
-and sources. A no-call and an absent genotype each get their
-own finding instead of a verdict, and a call without exactly two copies shows
-its copies without a homozygous or heterozygous label. The `reference` grant is
-read for one file, the assembly build the coordinate is reported on.
+The single variant from
+[04-cilantro-mini-rust](../04-cilantro-mini-rust/README.md), turned into a full
+report in the shape [06-reports.md](../../docs/06-reports.md) describes, with a
+finding, the evidence behind it, the method, its limitations and sources. A
+no-call and an absent genotype each get their own finding instead of a verdict,
+and a call without exactly two copies shows its copies without a homozygous or
+heterozygous label. The `reference` grant is read for one file, the assembly
+build the coordinate is reported on.
 
 ## Build and run
 

apps/05-drunk-o-type/README.md

@@ -2,8 +2,8 @@
 
 A panel of eleven variants, scored on three axes of how a body handles alcohol:
 flushing, reward and histamine. Each variant is its own `rsids/` grant, so the
-access pattern is [04-cilantro-mini-rust](../04-cilantro-mini-rust) repeated,
-and the owner sees every site by name before approving.
+access pattern is [04-cilantro-mini-rust](../04-cilantro-mini-rust/README.md)
+repeated, and the owner sees every site by name before approving.
 
 The app counts the allele each study tested, which isn't always the ALT allele.
 A missing allele or an absent genotype makes its axis inconclusive rather than

apps/06-genes-mini-c/README.md

@@ -1,9 +1,9 @@
 # 06 - genes-mini (C)
 
-[06-genes-mini-rust](../06-genes-mini-rust) written in C. It takes the sequence
-length from `stat`, reads each scalar into a buffer that grows to fit, and
-treats only `errno == ENOENT` as no answer. [01-hello-c](../01-hello-c) covers
-the toolchain.
+[06-genes-mini-rust](../06-genes-mini-rust/README.md) written in C. It takes the
+sequence length from `stat`, reads each scalar into a buffer that grows to fit,
+and treats only `errno == ENOENT` as no answer.
+[01-hello-c](../01-hello-c/README.md) covers the toolchain.
 
 ## Build and run
 

apps/06-genes-mini-go/README.md

@@ -1,8 +1,8 @@
 # 06 - genes-mini (Go)
 
-[06-genes-mini-rust](../06-genes-mini-rust) written in Go. It takes the sequence
-length from `os.Stat` and distinguishes an absent scalar from a failed read
-with `errors.Is(err, fs.ErrNotExist)`.
+[06-genes-mini-rust](../06-genes-mini-rust/README.md) written in Go. It takes
+the sequence length from `os.Stat` and distinguishes an absent scalar from a
+failed read with `errors.Is(err, fs.ErrNotExist)`.
 
 ## Build and run
 

apps/06-genes-mini-python/README.md

@@ -1,9 +1,10 @@
 # 06 - genes-mini (Python)
 
-[06-genes-mini-rust](../06-genes-mini-rust) written in Python. It takes the
-sequence length from `os.stat` and reads an absent scalar as no answer when
-`FileNotFoundError` arrives. [01-hello-python](../01-hello-python) covers what a
-Python module costs.
+[06-genes-mini-rust](../06-genes-mini-rust/README.md) written in Python. It
+takes the sequence length from `os.stat` and reads an absent scalar as no answer
+when `FileNotFoundError` arrives.
+[01-hello-python](../01-hello-python/README.md) covers what a Python module
+costs.
 
 ## Build and run
 

apps/06-genes-mini-rust/README.md

@@ -7,10 +7,11 @@ to fit in memory. An absent value prints as no answer, while a missing sequence
 is an error.
 
 The gene grant also covers the owner's `changes` in it, even though this mini
-doesn't read them. [06-bitter-meter](../06-bitter-meter) does.
+doesn't read them. [06-bitter-meter](../06-bitter-meter/README.md) does.
 
-The same mini exists in [Go](../06-genes-mini-go), [C](../06-genes-mini-c) and
-[Python](../06-genes-mini-python).
+The same mini exists in [Go](../06-genes-mini-go/README.md),
+[C](../06-genes-mini-c/README.md) and
+[Python](../06-genes-mini-python/README.md).
 
 ## Build and run
 

apps/07-powerhouse-of-the-cell/README.md

@@ -2,10 +2,10 @@
 
 A full report on the mitochondrial genome, read as one interval. It streams the
 `sequence` for GC content and density windows, and lists the owner's `changes`
-with a text map of where they fall. Like [06-bitter-meter](../06-bitter-meter),
-it counts listed positions without leaves and splits genotypes around symbolic
-and breakend alleles. It isn't a haplogroup caller, an ancestry test or a
-medical report.
+with a text map of where they fall. Like
+[06-bitter-meter](../06-bitter-meter/README.md), it counts listed positions
+without leaves and splits genotypes around symbolic and breakend alleles. It
+isn't a haplogroup caller, an ancestry test or a medical report.
 
 ## Build and run
 

apps/07-regions-mini-c/README.md

@@ -1,8 +1,8 @@
 # 07 - regions-mini (C)
 
-[07-regions-mini-rust](../07-regions-mini-rust) written in C. It reads the
-sequence in 8 KiB chunks with `fread`, so the interval never has to fit in
-memory. [01-hello-c](../01-hello-c) covers the toolchain.
+[07-regions-mini-rust](../07-regions-mini-rust/README.md) written in C. It reads
+the sequence in 8 KiB chunks with `fread`, so the interval never has to fit in
+memory. [01-hello-c](../01-hello-c/README.md) covers the toolchain.
 
 ## Build and run
 

apps/07-regions-mini-go/README.md

@@ -1,8 +1,8 @@
 # 07 - regions-mini (Go)
 
-[07-regions-mini-rust](../07-regions-mini-rust) written in Go. It reads the
-sequence in 8 KiB chunks with `os.File.Read`, so the interval never has to fit
-in memory.
+[07-regions-mini-rust](../07-regions-mini-rust/README.md) written in Go. It
+reads the sequence in 8 KiB chunks with `os.File.Read`, so the interval never
+has to fit in memory.
 
 ## Build and run
 

apps/07-regions-mini-python/README.md

@@ -1,8 +1,9 @@
 # 07 - regions-mini (Python)
 
-[07-regions-mini-rust](../07-regions-mini-rust) written in Python. It reads the
-sequence in 8 KiB chunks of bytes, so the interval never has to fit in memory.
-[01-hello-python](../01-hello-python) covers what a Python module costs.
+[07-regions-mini-rust](../07-regions-mini-rust/README.md) written in Python. It
+reads the sequence in 8 KiB chunks of bytes, so the interval never has to fit in
+memory. [01-hello-python](../01-hello-python/README.md) covers what a Python
+module costs.
 
 ## Build and run
 

apps/07-regions-mini-rust/README.md

@@ -6,10 +6,11 @@ its length and GC content, so memory use doesn't grow with the interval. A
 missing sequence or a failed read stops the app.
 
 The interval grant also covers the owner's `changes`, which
-[07-powerhouse-of-the-cell](../07-powerhouse-of-the-cell) lists.
+[07-powerhouse-of-the-cell](../07-powerhouse-of-the-cell/README.md) lists.
 
-The same mini exists in [Go](../07-regions-mini-go),
-[C](../07-regions-mini-c) and [Python](../07-regions-mini-python).
+The same mini exists in [Go](../07-regions-mini-go/README.md),
+[C](../07-regions-mini-c/README.md) and
+[Python](../07-regions-mini-python/README.md).
 
 ## Build and run
 

apps/08-vcf-mini-c/README.md

@@ -1,10 +1,10 @@
 # 08 - vcf-mini (C)
 
-[08-vcf-mini-rust](../08-vcf-mini-rust) written in C. It reads the call file
-with `getline`, which accepts long records while keeping only one line in
-memory, over a 64 KiB `setvbuf` buffer. The default buffer is small enough to
+[08-vcf-mini-rust](../08-vcf-mini-rust/README.md) written in C. It reads the
+call file with `getline`, which accepts long records while keeping only one line
+in memory, over a 64 KiB `setvbuf` buffer. The default buffer is small enough to
 make a whole-genome scan an order of magnitude slower.
-[01-hello-c](../01-hello-c) covers the toolchain.
+[01-hello-c](../01-hello-c/README.md) covers the toolchain.
 
 ## Build and run
 

apps/08-vcf-mini-go/README.md

@@ -1,8 +1,9 @@
 # 08 - vcf-mini (Go)
 
-[08-vcf-mini-rust](../08-vcf-mini-rust) written in Go. It reads the call file
-with `bufio.Reader.ReadString`, which accepts long records while keeping only
-one line in memory, over a 64 KiB buffer from `bufio.NewReaderSize`.
+[08-vcf-mini-rust](../08-vcf-mini-rust/README.md) written in Go. It reads the
+call file with `bufio.Reader.ReadString`, which accepts long records while
+keeping only one line in memory, over a 64 KiB buffer from
+`bufio.NewReaderSize`.
 
 ## Build and run
 

apps/08-vcf-mini-python/README.md

@@ -1,8 +1,9 @@
 # 08 - vcf-mini (Python)
 
-[08-vcf-mini-rust](../08-vcf-mini-rust) written in Python. Iterating the open
-file yields one line at a time, so a whole-genome call file never has to fit in
-memory. [01-hello-python](../01-hello-python) covers what a Python module costs.
+[08-vcf-mini-rust](../08-vcf-mini-rust/README.md) written in Python. Iterating
+the open file yields one line at a time, so a whole-genome call file never has
+to fit in memory. [01-hello-python](../01-hello-python/README.md) covers what a
+Python module costs.
 
 ## Build and run
 

apps/08-vcf-mini-rust/README.md

@@ -4,14 +4,15 @@ The app grants the whole call file, `v1/genome/snp-indel`, and streams `vcf` one
 line at a time to count its header lines and records. A whole-genome call file
 runs to gigabytes, far past an app's 128 MiB of memory, so it's never loaded
 whole. A failed read stops the app instead of reporting zero records.
-[08-vcf-roll-call](../08-vcf-roll-call) parses the same file with a library.
+[08-vcf-roll-call](../08-vcf-roll-call/README.md) parses the same file with a
+library.
 
 It reads through a 64 KiB buffer into one reused line. Both matter over
 millions of records, since every refill leaves the sandbox and a fresh line per
 record would allocate for each one.
 
-The same mini exists in [Go](../08-vcf-mini-go), [C](../08-vcf-mini-c) and
-[Python](../08-vcf-mini-python).
+The same mini exists in [Go](../08-vcf-mini-go/README.md),
+[C](../08-vcf-mini-c/README.md) and [Python](../08-vcf-mini-python/README.md).
 
 ## Build and run
 

docs/01-app-model.md

@@ -67,7 +67,7 @@ same report every time:
   unrelated to real time.
 
 An app that needs a random-looking choice derives it from its input.
-[10-fortune-cookie](../apps/10-fortune-cookie) does exactly that.
+[10-fortune-cookie](../apps/10-fortune-cookie/README.md) does exactly that.
 
 ## Limits
 

docs/02-manifest.md

@@ -23,8 +23,8 @@ category = "traits"
 license = "BSD-3-Clause"
 ```
 
-[04-cilantro-soapiness](../apps/04-cilantro-soapiness) prints this manifest,
-with a longer listing.
+[04-cilantro-soapiness](../apps/04-cilantro-soapiness/README.md) prints this
+manifest, with a longer listing.
 
 ## Format
 
@@ -120,7 +120,8 @@ It suits data that adds to a report without being needed for its answer.
   absent answer, as [04-reading-data.md](04-reading-data.md#least-privilege)
   shows.
 
-[02-permissions](../apps/02-permissions) asks for one optional variant.
+[02-permissions](../apps/02-permissions/README.md) asks for one optional
+variant.
 
 ## Choosing grants
 
@@ -170,7 +171,7 @@ per input and named after it, in UTF-8 with no trailing newline. A choice's file
 holds the picked choice. A multiple choice's file holds the picks one per line,
 in the order of `choices`, and is empty when nothing was picked. A text's file
 holds the text, which is never empty.
-[03-sundae-order](../apps/03-sundae-order) reads all three.
+[03-sundae-order](../apps/03-sundae-order/README.md) reads all three.
 
 Inputs never change what an app reads. An app whose reads depend on an answer
 grants everything the answer can select. The Ark's journal records which inputs