Broken Markdown-style link support

[sfgartland]

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Describe the bug

Markdown-style links does not appear to work for zk list or for the LSP.

Up to now I have used wikilink-style links for internal linking, but wanted to use markdown-style in some instances for readability. However, unless I have missed a config option, they do not seem to work. They do not show up in the zk list -l output and the LSP integration in helix returns "not found".

How to reproduce?

1. Add markdown-style link to existing file.
2. Use the lsp to check the link or run zk list -l [filename]

zk configuration

# zk configuration file
#
# Uncomment the properties you want to customize.

# NOTE SETTINGS
#
# Defines the default options used when generating new notes.
[note]

# Language used when writing notes.
# This is used to generate slugs or with date formats.
language = "en"

# The default title used for new note, if no `--title` flag is provided.
#default-title = "Untitled"

# Template used to generate a note's filename, without extension.
filename = "{{slug title}}"

# The file extension used for the notes.
extension = "md"

# Template used to generate a note's content.
# If not an absolute path or "~/unix/path", it's relative to .zk/templates/
template = "default.md"

# Path globs ignored while indexing existing notes.
#exclude = [
#    "drafts/*",
#    "log.md"
#]

# Configure random ID generation.

# The charset used for random IDs. You can use:
#   * letters: only letters from a to z.
#   * numbers: 0 to 9
#   * alphanum: letters + numbers
#   * hex: hexadecimal, from a to f and 0 to 9
#   * custom string: will use any character from the provided value
#id-charset = "alphanum"

# Length of the generated IDs.
#id-length = 4

# Letter case for the random IDs, among lower, upper or mixed.
#id-case = "lower"


# EXTRA VARIABLES
#
# A dictionary of variables you can use for any custom values when generating
# new notes. They are accessible in templates with {{extra.<key>}}
[extra]

#key = "value"


# GROUP OVERRIDES
#
# You can override global settings from [note] and [extra] for a particular
# group of notes by declaring a [group."<name>"] section.
#
# Specify the list of directories which will automatically belong to the group
# with the optional `paths` property.
#
# Omitting `paths` is equivalent to providing a single path equal to the name of
# the group. This can be useful to quickly declare a group by the name of the
# directory it applies to.

#[group."<NAME>"]
#paths = ["<DIR1>", "<DIR2>"]
#[group."<NAME>".note]
#filename = "{{format-date now}}"
#[group."<NAME>".extra]
#key = "value"


[group."sources"]
paths = ["sources"]
[group."sources".note]
filename = "@{{extra.author_last}}-{{extra.year_filename}}-{{extra.slug_title}}"


[group."sources/authors"]
paths = ["sources/authors"]
[group."sources/authors".note]
filename = "{{extra.author}}"

[group."main"]
paths = ["main"]
template="main.md"
[group."main".note]
filename = "{{slug title}}"

# MARKDOWN SETTINGS
[format.markdown]

# Format used to generate links between notes.
# Either "wiki", "markdown" or a custom template. Default is "markdown".

link-format = "markdown" # I have also tried wiki, but the issue persists

# Indicates whether a link's path will be percent-encoded.
# Defaults to true for "markdown" format and false for "wiki" format.
link-encode-path = false
# Indicates whether a link's path file extension will be removed.
# Defaults to true.
link-drop-extension = false

# Enable support for #hashtags.
hashtags = true
# Enable support for :colon:separated:tags:.
colon-tags = false
# Enable support for Bear's #multi-word tags#
# Hashtags must be enabled for multi-word tags to work.
multiword-tags = false


# EXTERNAL TOOLS
[tool]

# Default editor used to open notes. When not set, the EDITOR or VISUAL
# environment variables are used.
#editor = "vim"

# Pager used to scroll through long output. If you want to disable paging
# altogether, set it to an empty string "".
#pager = "less -FIRX"

# Command used to preview a note during interactive fzf mode.
# Set it to an empty string "" to disable preview.

# bat is a great tool to render Markdown document with syntax highlighting.
#https://github.com/sharkdp/bat
#fzf-preview = "bat -p --color always {-1}"


# LSP
#
#   Configure basic editor integration for LSP-compatible editors.
#   See https://zk-org.github.io/zk/tips/editors-integration.html
#
[lsp]

[lsp.diagnostics]
# Each diagnostic can have for value: none, hint, info, warning, error

# Report titles of wiki-links as hints.
#wiki-title = "hint"
# Warn for dead links between notes.
dead-link = "error"
# Warn when a note links to itself.
#self-link = "warning"
# Report missing backlinks
#missing-backlink = { level = "hint", position = "bottom" }


[lsp.completion]
# Customize the completion pop-up of your LSP client.

# Show the note title in the completion pop-up, or fallback on its path if empty.
#note-label = "{{title-or-path}}"
# Filter out the completion pop-up using the note title or its path.
#note-filter-text = "{{title}} {{path}}"
# Show the note filename without extension as detail.
#note-detail = "{{filename-stem}}"


# NAMED FILTERS
#
#    A named filter is a set of note filtering options used frequently together.
#
[filter]

# Matches the notes created the last two weeks. For example:
#    $ zk list recents --limit 15
#    $ zk edit recents --interactive
#recents = "--sort created- --created-after 'last two weeks'"


# COMMAND ALIASES
#
#   Aliases are user commands called with `zk <alias> [<flags>] [<args>]`.
#
#   The alias will be executed with `$SHELL -c`, please refer to your shell's
#   man page to see the available syntax. In most shells:
#     * $@ can be used to expand all the provided flags and arguments
#     * you can pipe commands together with the usual | character
#
[alias]
# Here are a few aliases to get you started.

# Shortcut to a command.
ls = "zk list $@"

# Default flags for an existing command.
#list = "zk list --quiet $@"

# Edit the last modified note.
editlast = "zk edit --limit 1 --sort modified- $@"

# Edit the notes selected interactively among the notes created the last two weeks.
# This alias doesn't take any argument, so we don't use $@.
recent = "zk edit --sort created- --created-after 'last two weeks' --interactive"

# Print paths separated with colons for the notes found with the given
# arguments. This can be useful to expand a complex search query into a flag
# taking only paths. For example:
#   zk list --link-to "`zk path -m potatoe`"
#path = "zk list --quiet --format {{path}} --delimiter , $@"

# Show a random note.
#lucky = "zk list --quiet --format full --sort random --limit 1"

# Returns the Git history for the notes found with the given arguments.
# Note the use of a pipe and the location of $@.
#hist = "zk list --format path --delimiter0 --quiet $@ | xargs -t -0 git log --patch --"

# Edit this configuration file.
conf = '$EDITOR "$ZK_NOTEBOOK_DIR/.zk/config.toml"'

e = "zk edit -s 'created' -i"




lit = "zk new --template literature.md --notebook-dir sources"

nlit = "python ./scripts/nlit.py"
nauthor = "python ./scripts/nauthor.py"
nlec = "python ./scripts/nlecture.py"
ncirc = "python ./scripts/ncirc.py"
nmain ="zk new --template main.md --title $@ main"
a = "python3 ./scripts/zllm.py $@"
process_handnotes = "python ./scripts/process_handnotes.py"


wc = "zk list --format '{{word-count}}\t{{title}}' --sort word-count $@"


log = "zk list --quiet --format path --delimiter0 $@ | xargs -0 git log --patch --"

Environment

zk 0.15.2
system: Linux 6.19.7-200.fc43.x86_64 x86_64 GNU/Linux

[tjex]

what do you mean they don't appear for zk list? list lists notes, not links.

I just tried to recreate this, but regardless of my link setting in the config, zk lists both outgoing links with ZkLinks -- even when one is in markdown format and the other in wiki.

e.g.,

# Untitled

[foo](7vx0)

[[yv2z]]

[sfgartland]

I've done some more testing and it turns out that wikilinks appear to resolve both relative to current file and relative to zettle root. However, markdown-style links only resolve relative to the current file.

what do you mean they don't appear for zk list? list lists notes, not links.

Regarding this, I meant using zk list -l test.md to find files linking to that file.

[sfgartland]

I've created a fix for the problem assisted by a LLM. Let me know if the quality is good enough to be merged into the code or if you spot any other issues.

Also, it is my first time actually contributing to a repo here on Github so please let me know if I need to do something more here.

Best wishes,
SG